1. I want to change resources so that they give a food/production/commerce bonus in whatever city they're in. Problem is, how do I do that?
2. How do I change how often a resource show up?

1. One of the XML files.
2. The map generating python scripts.

If it wasn't right before I go to bed I'd be more helpful, so sorry.

1 a bit more worked out :)
open CIV4BonusInfos.xml and you'll see the resources and stuff like that with a lot off code/junk under it. search for the yield tags (there are 3 in a row) and you can change these the number of your will. the line is as following (i think, not 100% sure): 1st yield=food, 2nd yield=production and 3rd=money

I think both of these can be answered by the CivIV wiki. If I was home I'd give it a whack, but I fear I'd confuse you and myself if I did it now... :)