How to use "Pay alone" option with credit memo.

Hi,

Example: Departments ----> A,B,C,D
Supplier-------->ABC Ltd.
1. Dept A has raised the invoice to the supplier in same day:ABC Ltd,
2. Dept B has raised the invoice to the supplier in same day :ABC Ltd
etc...

Now i need to give single check for one dept(A) with respective TDS deduction.
And same way need to give single check for another Dept (B) with respective TDS deduction.

we are making the Payments through Payment Batches.

How can i make the issue the single check for single invoice with TDS whenever the vendor have multiple invoices.

Thanks & Regards,