1. The key to most of this is understanding the licensing and coding for that.
In both Jira and Confluence, you need to look at the permissions. They both have a simple concept - "if a user can log in, then they count towards the licence number".
Off-the-shelf, you'll find that the groups "jira users" and "jira administrators" count as "can log in and hence count as a licence user" for Jira. Same for confluence, with groups similarly called "confluence users/admin". These are de-duplicated though - if my account belongs to both users and admins, it's still only one seat in use. Be aware that if you change these, it's the "can log in" that matters, whatever user/group scheme you decide to use.
However you implement your SSO, you just need to make sure the group memberships are following the rules (don't allow more than 500 in Confluence-users).
2. You will need to maintain your SSO code in-line with Atlassian releases. You don't *need* to keep up with Atlassian's releases of course, that's a matter of planning and resource for you. But you will need to check your SSO code on every release you decide to take.
3. That's a bit vague really. I'd start with the built-in application links and see how they work out for you.
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