If a company is your customer and a supplier . they owe you £5000 ( customer inv ) you owe them £10,000 supplier inv they say pay me £5000 can you do this on QB ?

Yes

receive payment on the invoice, and deposit to a cash type bank account

use pay bills and use the cash account to make a partial payment

then make an actual payment when ready

Hey eniblock, 

You can record this payment using a contra journal entry.

In the instance you have provided, you would need an open invoice on the customer with the £5000 balance, and an open bill on the supplier for £10,000.

You can then enter a journal entry (+ icon, Journal Entry) with the following details:

1) Enter the date 

2) On line one, under the account select your 'Debtors' account, enter the amount in the 'Debits' box,  and enter the customer under 'Name'

3) On the second line, under account select your 'Creditors' account, enter the amount in the 'Credits' box, and enter the customer under 'Name'

4) Save & close the journal entry

To link the journal enter to the invoice payment, go to the invoice and click 'Recieve Payment' and tick the journal entry under 'Credits'.

To apply to the bill, open the bill and 'Make Payment' then tick the journal entry under 'Credits'.