Line in audio from external source i.e. blu ray, or Mac always using xlr in's, records over modulated. Even when using comp or limit general setting. Do I need to use a pad to knock the signal down?

Yep! Get a decent audio interface that attaches to the PC with a USB connection and uses BALANCED lines to your mixer. I use a UA-25EX Roland/cakewalk as an example. (about $200 and there are cheaper units such as M-Audio Fast Track MKII ) Note these interfaces BOTH record and playback with two channels for stereo.
Essentially the audio board that is in PC's and Laptops are too near the switching noise of the processor and some of that is just bound to get into the audio lines as they don't even have balanced audio lines from the computers. Make sure you use either TRS or XLR balanced cables from whatever interface you get. Also connect ALL interconnected equipment to the same power source or receptacle. You can try to reduce the buzz with the mixer EQ's with what you have, but that sacrifices audio quality.

What is the source of the input signals? These need to be balanced lines and the sources need to be balanced. If you happen to be using condenser mics, you probably haven't turned on the Phantom Power in the mixer. If you are recording from a sound card in the PC, those have a lot of noise and are unbalanced and you have to use DI's with ground lift ahead of this mixer.

You will use microphone with balanced XLR connector into the XLR mic input. Note, the ALpha does NOT have phantom power so you cannot use condenser mics.

A guitar can be plugged into the hi-z instrument 1/4 inch jack on the left front of the unit.

To use the line 1/4 inch inputs you will use BALANCED TRS 1/4 inch cables from your source.for these channels. The level on these needs to be line level.

The line outs are for sending audio out to an amp. There appears to be RCA outputs you can use as well.

I am not sure what you mean by making your "amp record"... An amp PLAYS the audio, usually into a speaker.

If you are trying to play a guitar through your amp AND record, then you will connect your guitar to the Alpha, the amp input will have a cable from say Line 1 OUTPUT and when recording wou will have the echo feature on so your guitar is passed through to the amp.

These are hard to work on... but one possible thing is if you are using an XLR adapter that is going from balanced to unbalanced 1/4 inch plug. You need to go XLR to XLR on this one. The MONO adapters can ground out the signal as these things don't always drive balanced signals... The signals are also line level so one does NOT want to use an impedance converting adapter.
The preamp is mounted on the plate with the jacks and has pretty short leads that limits how far you can pull it out. Taking off the grille and removing the woofer to get access can be a pain, especially to get the grille back in with the rubber edging.
Of course there is always the possibilty that the driving op-amp on the preamp board could have been fried. Word of WARNING: Power ALL interconnected parts of your system from the SAME receptacle or source. Powering say a mixer from a receptacle at the back of the room and powered speakers from a receptacle at the front is a good way to have equipment fried by "ground bounce" on the power system. Run extension cord to your mixer from the front where speakers are powered!

Likely you haven't got the levels set properly. Start with the trim controls (head end gain) Make sure you are not clipping there. Also verify you aren't overdriving your amps. Remember that the outs are line level, not mic level so the gain oof following equipment needs to be set for line level.
ALWAYS USE balanced audio line from this unit... either XLR or TRS type cables. ALWAYS power ALL interconnected equipment from teh same receptacle or source to avoid ground bounce damage to circuitry. You don't say what you are using to record with. Make sure it has balanced inputs. For instance, connecting cables from this to the audio input jack of a PC which is unbalanced would be a disaster in audio quality. There would be a problem of levels and the unbalanced thing... You haven't given us enough information of your hardware configuration to analyze the problem more than what I have said here.

An insidious problem is if the throughput of your computer is being used up by things like anti-virus, anti spyware. Turn OFF ALL of these throughput hogs when doing audio operations. Also turn off wireless communication and ANY other active USB throughput hogs.

These hogs will usually cause sharp noises thaat are essentially discontinuities of the audio waveform.

IF the noise you are getting is a "hiss" type noise, that is different. That is USUALLY caused by the user failing to set the gains and levels properly. Some electronic noise is from the statistical background noise likited by the laws of physics, It is important to record and set the level well above these noise floor points.

Balancing gain is important. Set the amplitude of the line out to be near line level and lower the gain of following amplifiers. This is just good practice.

Anyway, decide which of these two noise sources might be what you are seeing.

The third noise MIGHT be from ground loop noise... for that power ALL, and I do mean all interconnected equipment from teh same power receptacle/source AND used balanced lines such as XLR or TRS wherever possible.

Using two balanced lines either TRS or XLR depending on what is on your M audiointerface, connect the L and R main outputs of the mixer to the L and R inputs of the M Audio. You will need recording software on your computer.

The key is to keep the guitar away from magnetic fields. Transformers in amps are a common source. You could use a graphic equalizer to "notch" out the power line frequency. Make sure your amp isn't the source of the hum by unplugging guitar cable. Then make sure the guitar cable is good by plugging it in and shorting the open end. Then plug into the guitar to check.

You may find your cable is sub-standard, or you MAY have to set yourself up to use balanced connections if your guitar has XLR output connector.

Sometimes the grounding of the conductive paint in the electronics well of the guitar gets ungrounded... check that using an ohmmeter.

Without knowing the resources you are connecting I cannot give you a schematic but will give this GENERAL advice:

1. Use BALANCED lines to connect from the mixer to your amps, preferably XLR connections.

2. Service the power to the amps and the mixer from the SAME place even if it means stringing a power cable alongside you audio cable snake.

It sounds like you have NOT connected via the recording software.
It is like the normal Windows software audio has hijacked the audio system even though it is external.

Go into your recording software and look for an option to select the Lexicon device. You did not tell us what recording software you are using.

This is not an uncommon problem with these external audio recording devices.