Uploading and create incoming invoices

I assume you are asking whether it is OK for two systems (your webshop and Dexxter) to generate new invoices. I don't think that's a problem, but there must be a single "list" of all your invoices, which must also be numbered consecutively. If I understand your situation as good, I would indeed upload every invoice from your webshop as a pDF to Dexxter under the option Income > Sales invoices > Upload invoice (top right).

That way, you can manage your sales invoices officially in just one system (Dexxter), and they will be neatly numbered.

Thank you, that does answer my question.