Not necessarily, depending on how chart of accounts is set-up, stock purchases might debit your purchases account, not your inventory - finished goods account. If that's what's happening in your case, changing the GL set redirection for inventory will gave no effect on day to day transactions.
There is a general ledger sets topic in the general ledger help file that goes through all the different types of automatic postings the system generates, so you can use this information as a guide.
Assuming your system is set-up to debit purchases and not stock on hand, what you actually need to do is set-up multiple purchases accounts. Then changing the purchases account on the applicable sets. If your chart uses opening/closing stock method, you would then need to set-up multiple opening/closing stock accounts as well.