You have 4 options that ship with the product:

1) Save the site as a template, with or without content. Content is limited to
a max of 20MB
2) smigrate, which will migrate  everything but users and permissions
3) FrontPage site export/import which is essentially the same as smigrate
4) stsadm backup/restore which is a full back with security, etc but cannot be
restored to the same server, and the users, etc must match

I have a question about what to do once you use stsadm.exe to get your
backup file. You have to migrate  it to the other server, but I have a
couple of questions before I do it:
I assume that you use 'smigrate', but 'what is not going to be
migrated once I bring it over to the other server?' For everything
that is not going to be migrated, is there another way to get this
information over to that server? Thanks so much for you help.

smigrate and stsadm are unrelated things - both have both an export/import or
backup/restore and you should restore using the same program you backed up with.
smigrate is a partial export/backup, stsadm is complete. Both are for WSS only,
for SPS you need spsbackup.exe instead.