We have a lot of lar files used for page and site templates in 6.0.6 and installed in a hook on start up.

Trying to load these onto a 6.1 system is creating a lot of errors.

is there a way to call the larImport code so it uses the old 6.0.6 "schema" for these files or at least to ignore certain errors?

If not how should we proceed with converting these lar files? Is there a document that walks you through the changes?
If we upgrade a 6.0.t site do these templates get automatically upgraded and if so can we create a lar export form the resulting site templates?

If I were you, that's what I would try out first of all. From what it sounds, this is your best bet. Provided that you succeed on upgrading 6.0.x to 6.1 of course!
And some notes:
-upgrade to 6.0.6 if not already at it and then to 6.1
-read forum posts about upgrade errors having to do with inconsistencies in data/images, etc, and watch out for gotchas before you try out anything
-DB backups ctra