Hi Kevin,
Technically you can disable Method's Engine and Listener from always accessing your QuickBooks file. However, this is not recommended because it defeats the purpose of Method. In doing so you are preventing real time synchronization. Also any data was entered in Method while QB was closed would only be transferred the next time you manually enable the Engine and Listener, likewise if data was entered in QuickBooks. Even so once you enable them you would have to exit out of QB and re-open it before it performs the sync also you risk duplication. In a nut shell, it is highly recommended that you allow the Engine and Listener to always access QuickBooks.
Regarding the slowness, have you checked if there are any scheduled reports that's coming from QuickBooks? Also have you checked the transaction history? You can review the following post on how to set the history - http://www.methodintegration.com/cs/forums/p/708/2366.aspx#2366
Hope this helps.