I would stick to doing it the simple way and separate the animations and stitch them together in a media program. Sure what you are asking can be done but may get very confusing to keep track of separate animations. You could set markers telling you what step or part of the animation you are on though. This being said editing or even replacing parts would become more confusing the larger the animation you have. My recommendation would be one assembly equals one animation especially if it is a larger assembly of parts. Not to mention separating will make for a smaller file size. The way I do it is make my animation and export as a series of high quality images and then import the images into Premiere Pro. There are of course many other options that are cheaper or even free as far as software. You will get a much better quality video doing it this way. Hope this helps a bit.
I would follow Derek's suggestion as well. I would create each of the videos separate and render them for separate files. You can use the same SMG file, you would simply save the smgSce file for each video timeline and start from scratch for each video.
Thanks guys, I appreciate the feedback.
Do either of you make use of scenarios to store your animations?