For Example:
A & B are the parties,

Here "A" uses Zoho books & "B" uses other than Zoho Books.

"A" sells the good "X" to "B" for 1000 on credit & "B" sells product "Y" to "A" for 1500.
Here "B" asks "A" to pay balance 500 so balance 1000 shall get set off.

But when i try to pass entry in manual journal it does not allow to pass the entry because you have not provided option of passing manual journals related to Accounts Receivable & Accounts Payable.

There is no option to adjust bill amount in the payments received, so that "B" cannot set off purchased bill from "A" of 1000.

So because of this "A" has to receive 1000 from "B" & "B" has to receive 1500 from "A" so that the accounts will be proper.

So here, if "A" asks that pay me 1000, then only my books can be made proper later i will pay you 1500. This doesn't sounds goods to "B".

In other software you can simply pass entry in the books of "A"

"B" Accounts Payable A/c 1500
"B" Accounts Receivable A/C 1000
Cash/Bank 500

My suggestion is,
Zoho books should make client easy to deal with his entries, it should not make hectic.

Note: If any solution has been existed for the above solution, kindly let me know & this wont be helpful only to the above example, there are so many kind of transactions for which the feature will be helpful.