How do I go about making the bottom of the cupcake out of fondant? I would appreciate any help.

I've never made one from fondant, but I can help you make it out of chocolate/candy melts. They turn out really cute with nice sharp creases.
Here's one I did:

http://cakecentral.com/gallery/2068977

Poohsmomma, I love it. Your cake is beautiful. Could you please tell me how you made the cupcake mold out of chocolate melts. Thank you very much.

I actually have a Nordic Ware pan, not a Wilton, but they're about the same. I just melted some candy melts, poured a little in the pan and rolled the pan around so the melted goo covered the entire pan. I used a paint brush to pull it up the sides. Also-You need to gently tap the pan on the counter to work out any air bubbles before you put it into the fridge. I repeated this to give it two coats and make sure it was covered well. I tapped it gently upside down on the counter and it popped right out...well the second one popped right out, the first one split!
I didn't actually bake a cake in the pan. I used a decorating bag to squirt some icing into the bottom of the finished shell and set a 6 " cake inside. I added a little more icing and another layer that I had trimmed to have a rounded top. That's what I put the rosettes on as the cupcake top.
Hope this helps.

I just made a candy shell for the first time, and it wa super easy! Same process she used. I did bake a cake in the bottom pan though, then carve down. I filed the cake first, then placed icing in the shell, set the cake in, then piped icing inside around it. Was quick and super easy!

http://cakecentral.com/gallery/2182712

I just bought the cupcake pan yesterday . Great pics and ideas. Thanks, can't wait to give it a try

thank you all very much for all the great tips. I will give it a try.

I think its easier to bake the cake, then pour chocolate ganache over it and let it harden.

I loved your cake Poohsmama and I really liked the inventive way to cover it! I would have thought fondant was the easiest and prettiest way to cover, but that was really awesome! Will have to try it soon! The ganache would probably be really easy too... thanks for some great ideas!

Thanks, but it's not my idea....read about it here on CC.

I have done it both ways - covered with fondant and also trimmed down and put inside a shell made from candy melts. Both ways work great. The fondant method requires a very thin layer of buttercream - just enough for the fondant to stick to and then you have to use a dowel or something to accentuate those ridges. Have fun!

My picture is hideous because it'd been out in the heat of the party by the time they took a picture of it:

http://cakecentral.com/gallery/2175325

But, I covered the bottom with fondant & pinched together to make the "pleats" of a cupcake liner.