What about using aufs?

Partition let's say 2Gb of the 32 gigs available. The procedure to install software would be this:
1. Decide to install software Not so obvious
2. Decide to install on the 2Gb partition
3. Apt installs it
a. remounts / as ro
b. mounts external partition as aufs on /
c. installs software
d. cleans some stuff (temp files-moves them on actual root)
e. remounts / as rw and mounts external partition as ro
f. flags software "installed on aufs"
4. Enjoy new software

admiral0