Just for some foundation, there are two main ways to populate the reference numbers for your transactions, either have Method create them or QuickBooks. There is an option in Method, located on QuickBooks->Sychronization, towards the bottom of the screen you will see a label for "Assign Ref Numbers in Method"? This is where you can choose to either have QuickBooks generate your transaction reference numbers, or QuickBooks.
I am not sure I can fully answer your question just because it might have to do with Accounting Principles I am not familiar with. Both QuickBooks and Method, when creating reference numbers automatically, treat each transaction differently, meaning they each have their own numbering system. So if you prefer to have them the same value (ie an Estimate and Sales Order), I just can't tell you if this would create any issues in regards to your books.
If you do wish to do something like this, I would suggest using the "Create Sales Order" button on the Estimate screen and make sure to include the Estimate RefNumber field so that you can use it to populate the SalesOrder RefNumber field when it loads the Sales Order screen.
Another option is to manually enter your reference numbers when you create your Transaction. You could also restart your numbering system in any transaction by manually entering a value when creating a new one, for example let's create an Estimate with a refNumber of 1050. The next time you go to create a new Esimate, it will go in order from the last number entered, so the next estimate, if not manually added at this point will be 1051.