how do i pay a subcontractor and for the cheque to show the 20% deducted which i can then monitor

Glad to have you here in the Community, @office34. 

Let's first turn on the CIS feature so you'll be able to track the 20% deduction when paying your subcontractor. 

Here's how to turn on CIS: 

1. Go to the Gear icon at the upper right.
2. Choose Account and Settings under Your Company. 
3. Select Advanced from the left menu. 
4. Click the Edit (Pencil) icon on the Construction Industry Scheme (CIS) section. 
5. Check the Enable CIS box. 
6. Enter your UTR no., Employer’s PAYE reference no., and Accounts Office reference no. 
7. Click Save. 
8. Select Done. 

If you haven't added a subcontractor in the program, you can perform the steps below: 

1. Go to Expenses from the left menu. 
2. Select Suppliers.
3. Find and click the supplier's name. 
4. Go to the Supplier Details tab. 
5. Click Edit. 
6. In the Supplier Information window, check the Is subcontractor box. 
7. In the CIS Information section, enter his UTR no., National Insurance no., verification no., CIS rate, and subcontractor type.
8. Click the Verify link. This way, HMRC will tell you all the necessary information when you verify your subcontractor, including his CIS rate.
9. Click Save. 

After that, you can create a bill or cheque for your subcontractor. QuickBooks will use his/her CIS rate to calculate the 20% deduction when paying him/her. You can also monitor them by running CIS reports and statements. 

For more information about the CIS in the system, here's a great article you can refer to: CIS in QuickBooks. 

That's it. You can always go back on this thread if you have other concerns. I'll be here to help, @office34.