2003 F350 charging woes

hello,I have a f350 powerstroke and I have run into some stupid luck on my part,I have run out of fuel a few times due to my stupidity,the problem is that after I fuel it up to get going it takes a while to get fuel back into the injectors,which in turn wears on the batteries.I have to have a jump start to make it happen.how can I tell if my alternator is bad and or is there a relay that might be involved that could be the problem of not getting a good charge on the batteries,which one battery do I jump to? thanks kirk