Firstly the regular VAT will be all sales you make with a place of supply in the UK, so most ‘physical’ sales unless you’re selling to business customers in the EU or exporting goods.
The MOSS is used for sales of digital services, since digital services are supplied where the purchaser lives using the MOSS stops you having to register in every EU member state. So your MOSS returns will split out your digital services sales to each member state.
In both cases if you’re on quarterly retruns that’s when you make the retrun and pay any tax. There’s only an annual VAT return if you registered for the Annual Return scheme, otherwise you submit and pay each quarter.
I would guess that any Annuakl Return you’re asking about is your normal tax return where you’ll pay either Corporation or Income Tax, this return is nothing to do with VAT, thats for different taxes.
I think that if you’ve signed up for both a normal VAT registration and a MOSS registration without really knowing what either is for the best thing you can do is have a talk with an accountant, there are really too many pitfalls here to deal with in a back and forth on an internet forum. Are you sure you needed to register for either of those scheme’s is your turnover high enough to require it, or did you just register because you thought that’s what businesses do?