I have just realised that my VAT returns are not including VAT to be returned on purchases, I have two companies within quickbooks and one is working fine the other not

The Community has you covered, @modelec.

Let's make sure that the VAT is set up on purchases. Here's how:

1. Navigate to the Taxes, and then select VAT.
2. Click the Edit VAT drop-down arrow, and then hit Edit rates.
3. If VAT for Purchases has not already been added, tap Add tax rate.
4. Tick the Purchases checkbox.
5. Enter a new tax rate a name, description, and percentage rate, then choose an account and determine which return line you want the tax amount to appear on.
6. Tap Save when done.

For more details, please see this article: Set up and record purchase taxes. 

Also, to have a summary of info for each box on the VAT return, you may pull up the VAT Summary Report. Let me walk you through the process:

1. Go to Taxes.
2. Click the arrow next to Prepare Return.
3. Select View Summary. 

You can always get back here if you have other concerns or questions about VAT on purchases in QBO. I'll be here to help you. Stay safe.