If you've done the wages jnl and posted the liability to the balance sheet - N/L code 2210 (PAYE) and 2211 (NI) - then the cheque needs posting against these two codes.
If you've just posted the net wages payment to N/L 7000, then you should post the PAYE to N/L 7000 too, and do a jnl to transfer the employers NI to N/L 7006.
I hope this explains, your post was a little vague so I've tried to cover the 2 common scenarios.
I Have posted the gross wages to N/C 7000, so i guess thats where i will post the PAYE to then? And then do a Journal to make the split. Is that correct. Thank you
If you've put GROSS wages to 7000, then you'll have done the jnl:
Dr wages Dr employers NI Cr PAYE Cr NI Cr net wages
If that's the case, you need to process the PAYE payment as 2 payments, one to PAYE and one to NI.
However, if you meant that you've put the NET wages to 7000, then yes post the PAYE there. You then need to do a jnl to transfer the employers NI to 7006.