My custom model has: head, left and right upper and lower arms, elbows, left and right upper and lower legs, knees, torso. Will I still be able to make my custom model have motor 6d and have custom animations like the "Dummy" here http://wiki.roblox.com/index.php?title=File:DummyPartHierarchy.png&filetimestamp=20140211231029
Yes. Instead of a humanoid, use an AnimationController (unless you want the player to be able to control it directly via client-side, in which case I think you still need to use a Humanoid).
In any case, I recommend these plugins:
Character Creator [BETA] by DaMrNelson
Animation Editor by ROBLOX
Use the first one to create the Motor6D joints and the second one to actually create the animation. Be sure to test simple ones first (ie just try moving a limb and making that run, save, and load) - I experienced a lot of crashing and loss of information before I figured out how to make it all work.