It depends on how many mods you have. If not that many, I recommend installing the premod and migrating your customizations. If you have extensive changes, then it's probably easier to apply the phpBB-seo mods one-by-one. There's nothing particularly different about applying this site's mods versus those on phpBB or elsewhere, except for the Apache rewrite module requirement (.htaccess changes).
METACOMMENT:
I recommend installing a local test server using XAMPP or equivalent. That way you can test in isolation then confidently move to phpBB-seo's solution. There are some webmasters who evidently apply mods to live boards. I suppose that's OK for very low traffic sites. Too often I read "HELP! My board is down!?!?" threads here and on phpBB.com (*). A good test environment and regular automated system backups can greatly reduce your chance of heart attack.
When I'm applying lots and lots of changes, I will test it locally using XAMPP lite
and on the hosted site. Sometimes there are subtle differences in the Apache / PHP / MySQL installations. It's really quite easy: Copy the live database to another database. Copy the phpBB installation to another directory. Update the .htaccess rewrite rules to allow for both installation (e.g., /forums and /forums301). Update the copied database CONFIG table to point to the new script location; it's also good to modify the cookie prefix setting too, so you can log into both installations in the same browser. Oh, and update the config.php of the copied installation to point to the copied database.
With the two installations, you can then test like crazy on the "semi live" board. When you're satisfied it's correct, simply rename the directories (e.g., /forums -> /forums-backup, forums3 -> /forums). Be aware some directories are writable, so they'll need to be resync'd (/files for attachments and the /images directory for avatars).
(*) OK, OK... I admit it, I've brought my board down a few times and learned the hard way how to avoid it - or at least how to recover quickly.
