My tax year runs from June to June will QuickBooks account automatically know this when i register my business or do i have to input this? Thanks.

I'll share with you the two scenarios regarding your concern, @dompinto. 

If you're trying to register your business for a new QuickBooks Online (QBO) account, you'll have to manually select June as the first month of the financial year. Let's go to the Advanced tab to complete this task. This way, your books cover the transactions from June to June. I'll guide you how. 

1. Go to the Settings (Gear) icon at the upper right. 
2. Select Account and settings under Your Company. 
3. Go to Advanced from the left menu. 
4. Click Accounting. 
5. Select June as the First month of financial year. 
6. Choose Same as financial year in the First month of tax year drop-down. 
7. Hit Save. 
8. Click Done. 

The screenshot below shows you the last six steps. 

I suggest visiting this website: Year-end Guide And Checklist. It contains important tasks to help you close the last year's books so you can easily start the current one. 

If you're referring to signing up your business for MTD through QBO, yes, the program automatically populates the tax year. Just enable MTD from the Taxes menu. You can also go back to the Advanced tab in the Account and Settings page. Then, click Learn how to connect in the Making Tax Digital section. View the screenshot below for your visual reference. 

Then, authorise the software to interact with HMRC. For the detailed instructions, see Step 2 through this article: Authorise QuickBooks To Interact With HMRC - MTD For Small Businesses. 

Once done, you'll be able to submit your annual VAT return to HMRC. 

I recommend running any VAT reports in QBO. One of them is VAT Summary. It lets you view the summary information for each box on the VAT return. 

I'll be right here to help if you need further assistance. Enjoy the rest of your weekend, @dompinto.