Paul,
I think you are making this way too hard

First, when you sync, you never have to hit the button twice. When you click on sync, it syncs both databases so they are the same. It works in both directions. (more specifics on this later).
There is a very good detailed manual in the wiki. Let me summarize here.
All that occurs is you have the main computer in the office, aka "Server." There is a database in your laptop, aka "Remote."
Connect to the laptop in whatever way you do, i.e. directly or through network, click on the sync button and browse to the remote's AmazingCharts.mdb database. It's that simple. It would need to be shared.
Now, at this point, you have two selections which basically answers your question. The default setting is:
Add remote updates to existing database.
This as the name implies will add any data you entered into the remote computer to the server. This is not helpful if ANY data was entered to the server computer while you were gone. I wouldn't see much use for this.
You can also click the next option, which is:
Merge two distinct databases.
This is what you are basically referrint to. Click on this radio button, press sync and at the end of the process you will have two identical databases.
What you may want to consider doing is go to any computer on your network other than the server. Change the path of that AC from the server's (real) database, and let it browse to the database in the AC folder on that computer, i.e. a database which does not have any real data. Copy that folder somewhere on your desktop or wherever. At that point, you will have two identical folders, the one in your C:\Program Files\Amazing Charts and the folder you copied. Enter a note or data into the database on C:\Program Files. Then change your path to the other folder and write some notes or add some patients. Change your path back to the folder on C:\Program Files. Now use your sync feature and browse to the database on the other folder you saved on your desktop. Sync the two databases. You can now connect to both databases and see they are the same. After you do this, play arond with it until you feel confident in the sync feature.