The reason for HMRC sending you an assessment is that you are late submitting your Vat Return. If you pay the assessment you could wait a very long time for them to correct the amount after you send in your Return, which is especially annoying if they owe you money!
What to do: Firstly, make some time to prepare your outstanding VAT Returns (or provide the necessary information to your accountant). Then submit any late Returns as soon as possible and pay the actual amounts due (if you can). If you do this within a few days of receiving it, you can ignore the VAT assessment.