Please help us to get the answer for these question.
1. As @nbhushan says, no, it would be a breach of your licence to remove or change the "powered by atlassian" bit, and the link behind it. It must be visible to the user on all pages where a footer appears (i.e. most of them). You can, however, move it around, remove the version and any other links you want, and add others. It is JUST the "powered by Atlassian" bit that it would be illegal to remove or change.
2. Yes, Confluence supports SSO, and linking from other applications. It exposes a REST interface for remote applications, and provides all sorts of other hooks for "integration". Without specific examples of what you mean by "integration", we can't tell you a lot more, but for the SSO at least, start with a read of https://confluence.atlassian.com/display/DEV/Single+Sign-on+Integration+with+JIRA+and+Confluence
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