Hello and welcome to Fish Forum!
Ew, three months in one of those little cups, what a mess. Good to hear you've at least go him out of that now.
The stickies at the top of the forum will be really helpful if you haven't gone through those already.
Bettas are best kept in tanks of 2.5 gallons or larger. They are also tropical fish, and thereby like warm water. The most important thing about keeping a betta (aside from clean water) is probably keeping a warm temperature. You can buy aquarium heaters from most pet stores, and some wal-marts may even carry them. Bettas are happiest in temperatures between 78 and 82 degrees, you will see an inmprovement in his activity level, and overall health.
Bettas come in a variety of colors, so it's not neccessarily unusual that he doesn't seem very colorful. Cellophane bettas are a color variation which pretty much lacks all pigment, and are see-through, you can see their internal organs. But if he's just pale and his colors are looking a bit washed out, a little TLC can fix that in a week or two. Bigger tank, clean water, warm water, and the right food will get him back into his full glory.
Food - I don't know if he came with food when you got him? Anyhow, bettas are carnivourous, and so normal fish flakes (which ar most ly vegetable matter) won't cut it for them. Betta pellets are what he needs, and it's a general consensus I believe that Hikari Betta Bio-gold is the best brand of pellets out there for them. A good diet is also known to help a betta regain their colors, but be careful, don't overfeed your betta, that can make him worse than he was before!