My recommendation is to not change the TopDir spec even for those version of BPC that allow it.

My approach is to have a dedicated filesystem for BPC's data, and ideally this should be one that allows for "live" in-use maintenance - expansion, disk swaps. LVM being a good example in low-end environments.

Just bind mount in fstab the partition you want to use for storage in the place where backuppc wants it (should be /var/lib/backuppc with the debian family packages).

Or put a symlink there pointing to the location you want, works just as well, as long as you remember it's "just" a symlink for any other tools you use that need to traverse it - IMO bind mounts are "lower level" and thus more transparent to user-space tools.

If you do this before the install, everything should land in the right place and get the right permissions. As you've seen the critical thing is that the pool/cpool/pc directories must all be in the same filesystem so
hardlinks can work and with versions before 3.2 you can't change the TOPDIR location after the initial setup

Don't be afraid to wipe and start over a few times while you're getting to know BPC, it's good practice. Note that once BPC is up and running you won't have to pay too much attention to it and you'll likely forget much of what you learned at this stage, so document everything you do and why you did it,

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I've also taken this a step further and moved my config and log folders to below TOPDIR so everything related to BackupPC is self-contained to the one filesystem. Note that as far as BPC is concerned everything appears to still remain in the expected filesystem locations, it's not aware of the bind mounts and/or symlink magic.

This allows the whole shebang to be easily transferred to a new host for maintenance/upgrade/disaster recovery situations, doesn't need to be the underlying OS, just (roughly) the same version of BPC - I've done testing moving from our production server (CentOS) to a "temporary restore server" on a generic desktop running both Ubuntu and even via a Live-CD-only Grml boot disc - (Grml is a system rescue CD package which bundles BackupPC) and everything "just worked".

To make this even easier, my LVM-over-RAID filesystem is self-contained in an external drive housing connected via eSata.

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Note that the latter bit isn't common, but the top AFAIK is normal practice. I'm a relative noob here, so if you read anything from the more experienced users posted here that contradicts anything I say, follow their advice.