project manager:
when you save a project, you can choose the COPY MEDIA WITH PROJECT tickbox in the Save dialogue and it will do exactly what you requested.
Sequences: Vegas does this with nested Veg project files.
Just create each sequence in its own copy of vegas (ie you can have multiple copies of vegas open at once, inclu one capturing or rendering while you work in another copy)
In the master file, just drop Veg files on the timeline much as you would any media. They can be edited the same as a normal media file.
Can also right click such a veg and edit the original.
🙂