Ok currently on PC and I have to give credit where it's due, I like the mod system on bethesda.net I like it alot more than messing around with 'other sites' and mod managers. However there are certain mods that will never be allowed on bethesda.net so I'm wondering if anybody has tried doing a mix and match yet?

EG: can I install a load of mods from bethesda.net and also manually add mods from another site, Will they work alongside each other, Will a mod manager cause issues with installed mods from bethesda.net etc?

Yes, manually installed mods work alongside the Bethesda.net mods. At least they do with Fallout 4 (the only manual mod I use is the one that allows you to get achievements while using mods, because I think it's absolutely ridiculous that achievements are locked even if you're only using mods like the Unofficial Patch).

good to know, thanks

No issues. You will be fine. BTW, Bethesda,net was a disaster for Fallout 4 PC mods. I suggest sticking with the Nexus.

Has anyone done a pre-compilation of mods yet, that work well with the SE? I would assume that mods that are of a graphical nature would/might overwrite the SE version!