Kev, that's because both the Q-Tron and Big Muff are sh*te. I'm not a big fan of either of them.
Running the Brown Dog into the 00Funk is no different from running any other fuzz into any other filter.
It's always given me some synthy Sir Psycho sounds. (Holy cow, that's some aliteration!)
The basic combination for synth sounds as most people would agree is, octaver->fuzz->filter. Take out the octaver, you've still got the majority of factors for synth sounds.
Previous combinations i've used are:
Boss ODB-3 and Q-Tron
Prunes and Custard and Maxon AF-9
Tonefactor Hellbaby and Maxon AF-9
Chunk Brown Dog and Chunk 00Funk
Prunes and Custard and 00Funk