you mean multiple allocation group??
i never seen this but i don't see an issue (or may be i am missing something what exactly you are looking for) as far as you manage the data properly.
as you see, when you create product allocation group you get the product allocation object automatically. so if you have different product allocation procedure, i hope you can have multiple allocation group. but assigning multiple allocation group with different allocation object might be issue.
Most IMP== try do a consistency check for product allocation after your complete configurations. It will give you the info is something wrong or should be looked in to.
APO-IMg-Advanced Planning and Optimization-Global Available-to-Promise (Global ATP)-Product Allocation-Check the Product Allocation Settings
As its always good, if you provide the requirement in details so we might be able to give better approach.
Please close the thread if issue resolved.
Regards,
Pravin M