I have a 2003 Deuce and my OEM battery went bad, when I would start it the check engine light would come on and then go off after about 30 seconds. Then it left me stranded, while driveing the bike went dead. I went and bought a battery from National Auto parts and the bike started, after a couple of days I would go to start it and would need to jump the bike to start it. Now when I ride it I can go for about 1 hour and if I turn it off I stuck, even if I jump it the battery wont hold enough power to ride for long what do I need to do?

G'day.
Sound very much like a low charge rate(your bike is not recharging the battery).
You need to have the bikes charge rate checked.
Basically-your bike should charge at a rate of 13.4- 14.2volts(DC) when running.
If it's not- the battery will keep going flat.
The test is performed by starting the bike & placing a voltmeter across the battery to measure the output.
It's a relativily quick & easy test to perform that only takes a few seconds-but if the charge rate is low then its caused usually by the regulator or the alternator(stator).
If you have a multimeter-or know someone who does-then the test is pritty easy & you need to do that before you go any further.
If you do it yourself- set the meter to Volts DC at a range higher than 15volts(if the meter is not auto-ranging) run the bike with the volt meter probes touching the Battery(black probe to battery negative-red test probe to battery posative) & observe the voltage reading.
You want 13.5 to 14.2v.
If you can't do it yourself then an auto-electrician or bike shop should be able to do it while you wait for just a few dollars.(only the test though- if the charge rate is low then you have then other issues to solve)

I hope this was of some help
Kind regards Andrew Porrelli