Hi Dane,
I have attached a link here to our Help Center Article on Payment Gateways. Take a look at the last bullet point on this page, it mentions that currently Method is only able process echeck payments through ElectraCash. I am sorry for any inconvenience this may cause you, I actually found a ticket we currently have in with our development team, to put a message on this on the actual screen suggesting it is not possible, or to not show the echeck option when using Intuit Merchant Services, I will add a note requesting it be taken care of.
-Ben