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It's up to you, but I have to agree that using different emails might be the best way especially if you think you might be losing the accounts later on.   Handing them over might be an issue in the future if you only use one account.  Who wants an angry and nasty client, after all?

Linking from a client site back to your site isn't a great way to go, even though the pages are related the topical relation is really from your project page to their site. I would have the usual clients/projects section on your site with links to your projects, but any link back from them to you should be nofollow. Having a site-wide footer link is not going to do you many favours anyway, and if it is just from their homepage footer it has less potential negative impact but is still not a real endorsement.