Question on reformatting my storage

Specs:

I5 8600k, OC’d to 4.5GHz Gigabyte Z370N WiFi Sapphire Pulse RX580 Vanilla Install

I currently have my system set up as a fusion drive, spread across a 250Gb m.2 and an 1TB ssd, so macOS reads the two as one logical volume totaling 1.25GB. I did this because I initially was planning on porting all of my files from a time machine backup and didn’t want to deal with the space inconsistency between the backup and m.2. At the time I only had my system installed on the m.2 and wasn’t utilizing the extra 1TB ssd. I’m thinking now I’d like to do either 1 of 2 things. 1: have my boot drive on the m.2 250gb /sdd and user folder on the 1TB ssd or 2: put my whole system on the 1TB sdd and maybe install Windows on the 250gb m.2. The reason why I’m considering this is because I have to use the AFPS.efi instead of the AFPSDriverloaderx64.efi and I also can’t get the clover pkg to update correctly. Even though it says it’s installed on the correct drive and will go through the installation/update process, clover doesn’t actually get updated. I’ve managed a workaround which involves installing clover to a GUID formatted usb and then copying over the newly created EFI folder onto my hard drive but I’d rather get away from having to do this work around every time I want to update. I’d like to “standardize” my system as much as is feasible. Anyway... long story short, I have a bootable clone of my boot drive that I made with CCC. If I erase both hdds, boot into my clone, and restore it to the freshly wiped 1TB HD will there be a problem that the copy was created from a system that was stored on more than one drive? Conversely if I wanted to put my boot on the 250gb m.2 ssd and have everything else on the 1gb ssd, how would I go about doing that given that the amount of data stored on my fusion drive has now surpassed the amount of space available on the m.2 drive?