Should I combine two 1Tb drives into one logical 2Tb drive or use one 1Tb drive for system/apps and move /users to the other 1Tb drive?  (I'd like ease of b/u too.)

Hello,
I have two 1Tb drives in my Mini, the first is full and the second one empty.  (I've been using the 2nd for Time Machine but the full source from dirve 1 soon has Time Machine complaining.)  I am contemplating whether to form one 2Tb logical drive from the two 1Tb drives or segregate their use, i.e. use the first 1Tb drive to hold the system and applications while moving the /users directory tree to the second 1Tb drive?
I'm assuming both are straight forward to do accomplish but have nagging doubts about segregating drive usage, will moving the /users directory tree to the second 1Tb drive:
impact apps which might otherwise expect to see particulat fies and directories in specific user related locations on the system drive;
hinder backing up (by having to setup two separate Time Machine activities)?
Finally, is there a better 3rt option?
Thanks,

Thanks and sorry Allan,
The supplementary questions would arise should I NOT chose to combine the separate drives into a larger logical one but to keep one of the two drives for system/apps and the other for users data...  I assumed that segregating drive usagel like this might reult in issues with apps which might expect to see some user directories/files on the same drive as the system/apps.  similarly, with two physical drives, I'd be looking to managing separate Time Mchines.  (I have a few 2Tb pocket drives for backups.)
Final question - if I do combine into a single logical drive (for system, apps, /users ... the whole lot), would I have any problem getting this logical one working from a Time Machine backup?  I ask that this backup was taken from the 1Tb physical drive and now I'd be looking to put it back onto a 2Tb logicl drive.
Thanks,

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