Is there a way to bill a customer for different items under different account sets?  In other words, can I have multiple account sets for one customer that can be billed on one invoice?

No

Why???

 My company sells two different products, each one assigned to a different g/l account.  We have customers that purchase both items and we want to be able to bill them on one invoice with the same customer number instead of having to generate two different invoices under two different customer numbers.  I think with Accpac 5.5 that we now have the capability of changing the account set for a customer when invoicing so we can use the same customer number instead of having to create a new one, but we would still need to generate different invoices for each item...is that correct?

Which side of the entry do you want to assign to a different GL account?

You can change the customer account set, but that applies to the whole invoice, you cannot change it at the invoice detail level. This changes the AR control account side of the entry.

Normally companies track sales by product using the category code, this will assign different sales accounts in the GL based on the category used for the item.