Hi there, taking the plunge to mod my v1 switch

so hi to this community

I do have a question to obtain the best 'clean experience' so I hope I do get my message across:
Q: Question about mixed content (legit and homebrew) when modding a Switch in use for several years:
Goal is to have emunand next to sysnand but what is the best practices before of after 'separating' these when the sysnand is already in use with several saves / installed games.
Is better to factory defaults a switch and then (soft) mod? So in this way there is no mess between 'legit' and 'homebrew' installations?
I do get the feeling that making a copy of my system (in use with several games installed) is not the most beautiful way in some sort OCD way. Also the separation between sys and emunand will grow when this dual system will be used?
I mean, for modding is is best practises to factory defaults the switch and then copy this to emunand so to have the sysnand (and installed 'homebrews') seperated?
Just wandering to reformat a Switch and then do the above, any thoughts?