Hey there,
I don't use the Boss VE, but I do use the Harmony GXT. As an option to the unit processing the guitar signal, there is a "through" jack for the guitar signal which means that the unit still "reads" the guitar but that signal is sent through the unit (dry, unaltered) for you to adjust gain (tone, etc) downstream, like at the console. Sorry if this is an obvious question, but have you looked at the instructions and checked what the various input options are for the Boss?
Edward