If you have to register for VAT then you will need to include your VAT registration number on your accounts.
PROFESSIONAL:
The VAT number is included in your registration key so you will have to contact us to regenerate you key and send it to you. Then you will have to ensure the VAT % is correct in System Variables. VAT is not held on each invoice but calculated when required. Note that the Professional version does not produce a valid TAX invoice. For info see the help files
SYNERGY:
Enter your new VAT number under Setup - System Variables together with the %. VAT will then be calculated and stored on all invoices. You can use the VAT initialisation function under Housekeeping to ensure that the changeover date is handled accurately in this regard.