Sounds like you're interested in bare metal programming. That's the intent behind Starterware:
http://processors.wiki.ti.com/index.php/StarterWare
If you're trying to poke various peripherals through CCS you must first enable the peripheral's corresponding clock through the PRCM. That's likely the immediate issue you're having though I recommend using something like Starterware in order to have more comprehensive examples as a starting point.
Unfortunately Starterware does not exist for AM35xx though you could likely leverage/port pieces of the code.