When using OS3.9 with BoingBag2 there shouldn't be a problem using a 36 GB partition, but if I were you I would install SFS or PFS on the harddrive.
Are you going to replace the 8.5 GB with the 36 GB, or is it only for backup?
I'm using a 76 GB partition on my own system, and no problems so far. As for the disk usage problem you mention; forget about it, as the program can't handle the large size drives...