There's no "should". In my situation, it was the Fender TBP-1 preamp that produced these immense low end frequencies - therefore it was no use to put the MicroThumpinator on the pedalboard. As soon as I put it in the fx loop, the unwanted low end produced by the eq section is reduced significantly and the whole setup works perfect.
In the loop is also the dbx 160A, which is placed after the Thump because there's no need to compress those frequencies.
Works charming this way.
I'd find an effect where without the MicroThumpinator your cab just freaks out just like in the vid on the sfx homepage. Then try it with different positions and decide after.
That way you'll find the perfect signal chain. Do report what you've found out!