Installed SKSE using it's own Installer, do I need to restart from scratch?

[blingblaow2]

Before I read any guides to modding, I was pretty much just winging things, and I managed to get a reasonably working setup without ever installing SKSE properly. Instead, I installed it using it's own installer, rather than manually and then linking it through MO. Now I've started to develop issues with the overwrite folder and SKSE requiring mods. Will I need to delete everything and reinstall from scratch, or can I just reinstall it "properly" and move the appropriate files into a different directory, or something like that?

[GrantSP]

The actual SKSE plugin can be installed via its own installer or manually so long as it exists in the "Data" directory of Skyrim.

The scripts that accompany SKSE should be installed into MO as a mod so that they can be manipulated in the order if needed.

 

The so-called "issues" you mention are probably nothing at all and just the result of mods creating new files after the game or some tools are run. Just move those files into an existing mod that matches the output or create a new mod from 'Overwrite'.