@JKM@SA - To add to what Ted already mentioned, I think you need to take into consideration how many documents you are expecting to upload in the log run. If your document uploads will be low and you don't care about seeing these documents in QuickBooks (if you're using the desktop version) then sticking with the native document upload in Method is fine.
If you're going to start uploading regularly to Method and want these uploaded documents to appear in QuickBooks (via the SmartVault toolbar) for customers, invoices, etc., I'd recommend using SmartVault. Their storage costs are low and while most Method users never reach their storage limits, if you start uploading a lot of documents, it can add up very quickly. There is also no migration of document uploads from Method to SmartVault. This means if you start uploading to Method directly and want to move these to SmartVault, it will be a manual process.
Danny