I don't believe you can associate them with assets. At least I never have. If you have 10 assets with original value of 10k and current value of 6k, you just put in an entry to the proper Fixed Assets accounts in those amounts as a regular journal entry. Then once the assets start depreciating, the entries generated by FAM will be properly linked.
You could try linking the manual entries to the Acquisition and life-to-date depreciation records via CSV, but I'm not sure that would work. And there are all sorts of background records with FAM that might not update properly, so I probably wouldn't mess with it. Just maybe make a note somewhere (maybe as a note on the FAM asset records themselves?) what the manual entries were.
If you do try to link them via CSV, I'd test extensively in Sandbox first, including running the following month's depreciation to ensure something doesn't get screwed up when you try that.