Hello,
Well, actually no... Mach 3 cannot generate paths. It can with wizards generate 2D and 2.5D toolpaths, and with Lazycam too, but not 3d toolpaths certainly not 5 or 6 axis.
Mach 3 will do what you tell it to do, so you need a CAM package to do the toolpaths,
5 axis CAM packages are expensive since they need to calculate tool offsets in 5 axis, there are a few out there. A freeware cam plugin is available for 3DS MAX, GMAX and Autodesk VIZ, it is called CNC Toolkit
http://groups.yahoo.com/group/CNC_Toolkit/It works but it has a steep learning curve but it does work.
Now Indexing vs continuous:
Indexing refers to having some axes still while machining with the remaining ones. One example would be a 4th axis rotary table. you machine with 3 axis while holding the rotary table still, then turn the rotary 90 degrees and then machine again in 3 axis, then turn it another 90 degrees and machine again etc..etc..
Continuous is when all axes are moving at the same time.
Now with your control box, heatsinks are a must if your steppers are above 3 amps i think, but it is a good idea to have them even if its under that. you have 5 geckos mounted on your box, and you say you still need to mount TWO geckos more? that would be 7 geckos, and mach can only handle 6 with dual parallel ports.
Regards
Fernando