Welcome to the community! I've been a bit MIA during this pre-tax season, but usually people just respond to questions right away.
As some of the others mentioned, I'm in the bookkeeping/back office ecosystem space for independent restaurants and bars. I have not specifically done a square to QBO via commercesync hook up. But it's actually something I've been waiting for a chance to test out.
Usually they will walk you through the process... it's all about mapping the POS items correctly to accounts and/or items within Quickbooks.
One thing I will say, from experience POS salespeople/tech help aren't really going to talk you through your POS set up in terms of architecture. In other words, to have a good sync that makes sense, your POS 'map' has to make internal sense to what you want to collect from it. Like a table of contents sort of. Likewise, when you translate that data via commercesync, your QBO set up has to make sense, and it has to do it three ways!
1. CAPTURE Things in Square that you've taken the time to set up right need to continue to have integrity in the way they are placed in Quickbooks by commercesync.
2. CONSOLIDATE Things in Quickbooks need to be able to interpret commercesync correctly, keeping in mind that platform's capabilities and idiosyncrasies.
3. REPORT Finally, Quickbooks needs to be set up in such a way that it can "spit out" information that makes sense to you and your client.
This all is not as complicated as it sounds, you just have to sort of decide in advance what you want to capture, what you want to consolidate, and what you want to report. Things like categories of sales, discount types, time of day sales, parent / child totals for some categories, etc. etc.
You can only track in QBO what you've tracked in Square and brought over through Commercesync. Once things get put into categories or combined in accounts, it's more difficult to tease that information apart again.
My advice: have a conversation with your client on the structure of both the POS and QBO related to what they want to see for operations. And don't forget what will need to be used for all the tax and official reporting needs too!