That will work Just fine.
You don't even have to have in groups of 3 and if you wanted to, you could even use bottle Chem 1 then bottle Chem 4 then bottle Chem x.... Not that you would want to but I'm just showing you the flexibility you have.
The only thing I strongly suggest is keeping good notes to as what each custom program you have for which process.
I use Chem bottles 1-4 for B/W and Chem Bottles 5 and 6 for C-41.