Hi Haiden,
I'm going to try to aswer each of your questions individually.
"How does this get impacted if there are multiple QuickBooks files beginning used with separate Method accounts for each?"
You can have multiple QB files installed on the same computer. The sync engine will launch for the right account when the company file is opened.
"Is the main syncing computer the first PC where the Method Sync engine got installed? Can this be changed?"
Initially yes, it is the first computer to sync to Method. You can change this at any time. There is a button on the QuickBooks > Synchronize page where you can reset the main computer to sync with. When this is reset, then the next computer to complete a full sync will become the main syncing computer.
"Is the main syncing computer the first PC where the Method Sync engine got installed? Can this be changed?"
In short, yes. Method will look to the main computer to do the syncing. Unless this is reset (with the button from above) than all of the main syncing will happen on the main computer.
"In regard to having multiple QuickBooks files in use; if the main computer or the other PCs have a second company file open am I corrrect that syncing will not occur?"
You are correct, it will not. The sync engine will not connect to the account. It may launch, but there will be no Method credentials in the sync engine. Also, along with the "main syncing computer" there is also the "QuickBooks file to sync with". Method will not sync a file that doesn't match this. Rarely should this ever be reset.
"What is the best practice with multiple Quick Books files to prevent syncing problems?"
There really shouldn't be any syncing problems. Since the sync engine will relaunch with with each company file with the correct Method credentials for each account, there really isn't any best practice to follow. I've run multiple test files on the same machine here for my test accounts and never had an issue.
Hope this helps,
Adam