Managing ports on ViaVerio VPS v2 server

[Tom Munro Glass]

I have recently migrated from a VPS v1 to VPS v2 server, and with it comes the 
advantage of being able to install software from ports. One of the first 
things I installed was portupgrade, thinking I would be able to manage future 
installations and upgrades in the normal way.

The problem is that some software, in particular Apache and Perl, is 
preinstalled and possibly tweaked for the Virtual Private Server environment. 
So when I try and run portupgrade I get loads of "stale dependency" messages. 
For example, I installed SpamAssassin 2.63 some time ago, and I have tried 
using portupgrade to upgrade to 2.64, but it won't work.

My questions are:

1) how should I manage ports in this environment?

2) should I use cpan instead of portinstall/portupgrade to manage perl 
modules?

Regards,

Tom Munro Glass