I have created a sync from another system we use in the business, which will copy all the customer accounts and employees to SuiteCRM.
I have also created a UserID field in the user module, and created a OwnerID field in the Account module. These fields are also copied from our other system which creates a link between the User and the Account records
Assuming I use a workflow, how do I assign users to the accounts by matching the UserID and OwnerID fields from the two records?
Personally, If you have a custom system for importing the data why not do that change there? If you move away from the system that’s one less custom field needed for already existing functionality. In your sync simply replace the values in the assignedto field with the corsponding user id and your problem is solved. The other option that I would go with if this will be a one time only run is to write yourself a nice little SQL script which does the same and babam problems solved.
Workflows are super useful and could definitely achieve this fix but In this cause you may find other methods more reliable and easier to do 
I’m using an online sync tool that will copy my data from my other system to SuiteCRM, although it doesnt have the ability to lookup the ID for that account, contact etc and save that to the record, it is just a simple copy
We would be importing the third party ID field anyway so if we could make a workflow to use this field to link the records that would be much easier to maintain then running a sql script