Sebastian:
Your 3rd party auditor should publish a schedule/agenda of what they want to audit, before they do the SA. If they didn't, you must ask for one. It is acceptable to internally audit those items, before your SA. In fact, you must also get a schedule/agenda so that you know who in your organization needs to be prepared and so that they are available to meet the auditor during the SA visit.
Otherwise, your normal internal audit schedule should be continued as planned. You don't need to worry about having done all processes before the SA - unless your 3rd party auditor has their spin on things - but you don't have to accept that!
Good luck!
Andy