Dave,
QB doesn't support export of ALL custom fields through the SDK or ODBC connection, so you might not be able to use all of your custom fields in Method. For example, the new custom fields added in QB V10 are not supported by QB and therefore unavailable to Method.
I believe there is some support for the original 5 custom fields in QB, but that might also be QB version dependent etc.
The most comprehensive characterization of the support from QB for the newest releases can be found at this blog entry by Charlie Russell.
http://qbblog.ccrsoftware.info/2009/10/custom-fields-in-quickbooks-enterprise-10/
I have also posted this question to this board. It should be easy to find by scrolling down or searching for "custom fields enterprise".
Custom field support from QB has been crummy from as far back as 2004, the first time I characterized them for IIF import/export and report writing. Be careful with them.
I believe this could be one of the key reasons why Method is necessary and a lifesaver for adding functionality to QB as additional field data can be held in Method with only the posting data needing to be synch'd.
Cheers,
James