They won't merge. You'll either have to update your 3.5.4 template to be compatible with 3.6.0 or you'll have to download a new theme that's designed for 3.6.0.
If you're concerned about upgrading, the best thing to do is setup a Test Board and "test" upgrade. There's a tutorial on setting a Test Board up on your local PC or you could just duplicate your SQL DB and setup a new forum on your server.
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