One common question we see from MyWorks Sync users is to ask for suggestions on better identifying/grouping the orders that MyWorks Sync sends to QuickBooks from WooCommerce - and telling them apart from other orders already in QuickBooks. The following practices can be helpful tips on how to best segment / report / identify orders MyWorks syncs into QuickBooks - although we always suggest including an accountant on decisions like this, as they'd most likely be able to suggest the best practice you adopt.
Using Class or Location for reporting
By default, MyWorks Sync does support setting a QuickBooks Class or Location (can be named differently in QuickBooks Settings) to sync all WooCommerce orders to in MyWorks Sync > Settings > Order > Default QuickBooks Class or Default QuickBooks Location.
Often users will create a class called "web sales" in QuickBooks, for example, and then build out their QuickBooks reporting based on this class they set to be used for orders synced to QuickBooks by MyWorks.
Using custom fields
MyWorks Sync supports custom field mapping - which can send a value, or specific WooCommerce order field - into a specific field in a QuickBooks order (Memo - message on invoice / your own custom QuickBooks field). Some users opt to have a value like "Web Sale" be custom mapped to one of these fields in QuickBooks - in which case QuickBooks reporting can then be filtered utilizing this specific field.
A similar example of using custom fields would be to have the WooCommerce Order ID be synced to one of the above mentioned fields in QuickBooks - and QuickBooks reporting can then be used based on whether or not this field contains a value for an order.