Sounds cool!
I would definitely get familiar with a 3D solid modeling program. 2D programs like Autocad are fine for working out geometries, but even the sketch mode in most 3D modelers will be way more suited for what you want to do.
There is nothing wrong with a single pivot bike - What you need to do before you even think about designing is write down your goals for the bike. If you just start throwing pivots and swingarms into the modeler, you will most likely end up with something pretty un-impressive. I would REALLY rercomend that you figure out what you want your frame to do. NO ONE FRAME IS PERFECT. No one frame can be the best at everything. Even really, really expensive frames have comprimises somewhere in them. You can not have the best pedalling, best braking, most neutral, stiffest rear end, most plush, most low speed maneuverability, most durable and lightest frame on the market.
So, write down your primary goals: Do you want to keep the design simple, light, and easy to manufacturer? Then your single pivot will be an excellent choice. Do you want to make the bike neutral in braking bumps? Then you will need some type of rear floating brake (either a floating caliper or as part of a four bar suspension system).
Once you've got your goals, then go check out EVERY website that you can find to ensure that you're at least within the right area as far as geometry is concerned.
Now, you can begin to start the design process. If you're in school, you should use whatever 3D CAD software you can get access to for cheap/free. The two main programs that you'll find in the industry will be Solidworks and Pro-Engineer. Catia is very sophisticated, but prohibitively expensive if you have to buy it commercially - student packages are a entirely different story though
Also, keep in mind your manufacturing capabilities. If you're making these with your own money and labour, remember that any CNC maching that you require will be VERY expensive. You should be able to make most of your parts manually unless you have access to cheap/free CNC machining. Also, you'll want to find a good welder (preferably someone who actually welds bikes), and again, they will charge you an hourly rate which will not be cheap.
Finally, you'll need to find a heat treater (if you're making it out of aluminum) once it's welded. I would recomend that you use with 6061 Aluminum, or standard 4130 Cr-Mo. There is excellent availability of those materials, especially 6061 Al.
I hope that helps. Oh ya, find out as much as you can about suspension design, then do vector force diagrams (or do it in your solid modeler) to understand what impact your design decisions will have on your frame. Finally, don't build the first frame you design - you'll be suprized how many design changes you can come up with once you let your first revision sit for a few weeks.
Good luck and don't forget to show it off here once you're done!