Hi Caren. Long time no "see"!
At 214, we originally considered implementing a separate sub-domain for each of our school/building sites but before officially rolling out, we decided on using one sub-domain for all students (ex:
stude...@stu.d214.org) and the main domain for all staff (ex:
brian....@d214.org). We wanted separation mainly for management purposes to make it easier for devising scripts, etc. as well as the ability to manage or apply different policies, filters, etc. We still maintain the accounts in separate orgs in Google Apps, synced automatically with our directory. This has so far worked well for us for over a year now but sometimes there are issues with students being able to access Sites or Docs shared by staff members. I think we've resolved that for the most part but it may be something to keep in mind as you lay things out.