I never was able to get programs to stay between boots. only settings. I just use the hard drive install if im using DSL...and DSL-N I use the Frugal HD Install.
The packages themselfs for programs are not that big. Typical programs are usually only a few mb.
You can always just enable apt-get and apt the packages if you need to. apt is probally one of the quickest and easiest ways to get programs
Code:
apt-get install *packagename*
As for the backup file, it shouldnt be that big. I couldnt imagine it being more then 100MB if you have a bunch of stuff in it. But I do think that the backup file has to be on a different medium then what you boot DSL off of. With the hard drive install, there is no need for a backup file, so look at doing the HD install.