They will have to be updated one by one manually. Depending on the module, it may be easily recreated within 8.x without any custom code (aspx, ascx, etc.).
As long as you follow the upgrade procedure (5.5r2 -> 6, 6 -> 7, 7 -> 8) and ensure you run your site at each upgrade point as it updates the database. 5.5 to 6 and 7 to 8 have significant API changes so you'll want to keep those in mind.
I just ran an upgrade from v6 - v8.2 in aspx mode and it took about 24 hours of evaluating, running the upgrade, backing the upgrade out, running it again and making code changes. I estimate I still have about 10 hours left. Depending on the amount of custom code you have it will vary but be sure to give yourself plenty of time for testing, especially if you have custom code.