What happens if you put a silver fossil on a dino that has a gold fossil..

A dino can only have one super fossil at a time. If you offer a fossil to dino that already has one, a box will pop up telling you what the stats will change to and asking if you want to go ahead with the addition. If you go ahead and give the fossil to that dino, the original super fossil just disappears. While you can only have one vivosaur of each number at a time in your holder, (and yes, the evolved forms of any given vivosaur count as your one copy of that number) you can bank a vivosaur out of your holder into your bank, collect another copy of that vivosaur and give that copy a different super fossil. When making teams, you can choose from both your holder and your bank. (If you wanted, you could have a team with three T-Rexes on it, though why you'd want to with Rex's neg. Effects on the AZ I don't know!)
Hope this helps.