Ahhh gotcha. It really depends on what you want to do. I use a Voodoo Lab Amp Selector pedal that allows me to mix and match up to 4 amps in any configuration. It has ground lifts to prevent/eliminate and grounding issues that may occur when you blend amps.
For the most part you will need a decent ABY pedal such as the aformentioned Voodoo Lab but others are very nice as well. Lehle, Radial Engineering, Whirlwind, and Framptone make some very nice stuff. Again, ground lifts are REALLY helpful.
If you are running combos you don't have to really worry about phasing issues and other problems that may occur with heads. However if you are wanting to use 2 or more heads you need to have either a stereo cab or 2 seperate cabinets. I used 2 100w heads into a stereo 4x12 Fender cab rated at 300w. So I had 50w to spare on each side without risking hurting my speakers or amplifiers. When you run 4x12 cab in stereo keep in mind you are basically veritcally splitting it into 2 2x12 columns. MAKE SURE the speakers have ample wattage ratings. Ohms selection is also important. I would run my heads at 8ohms a piece into the cab (each set of 12's at 8ohms as well).
It sounds complicated but really all you need is a guitar, a cord to plug into the ABY pedal of your choice, and two long cables to plug into your amps. You can experiment with placing overdrives before or after the ABY for different results. Joe has mentioned that he likes to sometimes push an amp with a mid heavy Tubescreamer type pedal on one amp only to make the mids stand out (usually on Marshall plexi type amps). That was before he got the midboost mod on his Category 5 plexis. Good luck and feel free to ask any more questions!
'67 and '74 Fender Twin Reverbs, '74 Marshall 1987 lead mkII, Metro Superlead 100. Pedals from TC Electronic, Ibanez, Dunlop, BK Butler, Electro-Harmonix, Fulltone, Maestro/Gibson, Loopmaster switching, VoodooLab, Boss. Gibson and Fender guitars, Dimarzio pickups.