My check engine light is on and sometimes my car won't start.

IF it still has the original battery, that may be the trouble... The alternator output, the battery and 'possible' parasitic load (something draining the battery) need to be tested!!!

It sounds like sulfation has occurred in one or more cells of the battery. Try overnight charging on medium, then Charge the battery every night on low for a few days. See if it gets rid of it. If you can access the cells , use a digital voltmeter & check cell voltage to see if any one of the cells have a big voltage difference from the rest.