Should I be building everything in one design?: Fusion was designed with a "make everything in one go" state of mind, so creating a complete design is, more often then not, done in one file. You CAN create separate files for each of your major designs and then bring them in and assemble them. But if you do that, why not just use Inventor?
Should I put each component in a different folder?: If you do not plan on creating "Drawings" from the designs, I would make sub-components out of the related components. If you intend on creating "Drawings" from them, and use the BOM table, the sub-assemblies will not show up. I believe they are working on that though.
Should I always always put joints in all my bodies?: You cannot use joints on bodies, you have to use them on components. You don't have to but you can. Even on things that do not plan on moving, I sometimes create a joint just so I can move everything around willy nilly and when i am done I can use the "Go to home position" option and everything goes back in its place.
Should I never delete a component? Typically, you do not want to delete a component. Unless you know FOR CERTAIN that it is not tied to anything, use "Remove". Otherwise you can get unforeseen consequences downstream.
Should I be very careful of the starting location of the design, (x,y,z)? and how future components relate to this point? I try to keep my bodies at the origin because it is easier to figure out where the position of the geometry is going to go when you use joints. Keep in mind that there is a difference between moving bodies and moving components.
_________________________________________________________________________________________________________________________________________Forever yours,
Love,
Brian
PS. If this answered your question, please mark as answered so others do not read through the posts trying to figure out if it was answered.