StewMac have all the colors, dyes, stains, glues, finishes etc. that you can imagine. If you're not sure, send them a mail with your questions and pics of your guitar, they're usually very helpful. Their stuff is not the cheapest, but they offer quality and you can be sure it'll work as advertized. Also those Dan Erlewine tutorial vids are pure gold.
Depending on the depth, you can do it with superglue, drop fill some lacquer or sometimes shellac if not too deep. Sometimes even nail lacquer will do, but I'm not a freind of that - the quality varies and sometimes it can end up like with cheap rattlecan finish with cracking and whatnot later.
If it's yout first time, it helps if you have some less important object for experimenting before you do the actual guitar.