When it comes to Skyrim, whatever mods you start with, should be kept through the whole playthrough. Incorporating mods late into a playthrough is not ideal as well. Sadly, this isn't TES3/4 or FO3/NV, where you could get a true clean save. A true save cleaner doesn't exist for Skyrim. But in this case, my personal opinion is to wait until the stable version is out, then starting fresh. 1.59c installs itself atm, where afaik 1.6 is planned to be started through MCM (more mods need this). Not saying you won't be able to upgrade from 1.59c to 1.6, but if you plan to have as clean and safe of a playthrough as possible, I'd advise to wait.