There are no hard rules for how to hook the stompboxes up because ultimately you should try different things and do the one which sounds the best to you.
Having said that, what you mentioned is a good way to start: TimeFactor in the parallel loop and ModFactor in front of the amp. Be sure to enable Killdry on the TimeFactor as this will properly mix only the wet signal into your sound. Killdry is found in the Bypass section of System Mode.
Due to the nature of some of ModFactor's effects, certain settings may alter the volume. This could be the case with any extreme Modfilter and Q-wah settings, etc. Generally this should not be a problem though.