In the big scheme of things, there's not much special to say about hunting DSOs with a Questar 3.5".
Subject selection: Anything suitable for a 3.5" Mak (c. 3" refractor, in terms of light gathering). If you include double stars in the category of DSOs, the exceptionally fine optical quality means that you can jack up the magnification to see if you can detect challenging double stars. Also, there have been a couple of threads in this forum about viewing carbon stars (which can be done with any other scope, of course).
Best season: No different than for any other scope
Eyepiece selection: Use the same guidance as for other scopes. Some DSOs need low power (e.g., the 24 mm Brandon) due to low surface brightness, but others (some planetary nebulae, globular clusters) can benefit from a higher power, such as the 16 mm Brandon, maybe even with the barlow.
Filter selection: I don't use any for DSO, so I cannot comment on this.
Finder use: Here is where Questar is unique. Some people don't like the Q's finder and either use setting circles (requiring a bit more care and effort during setup) or mount another finder device, such as a red dot finder. If you are comfortable with the Q's finder, it takes practice getting used to the huge field of view (e.g., 12 degrees with the 24 mm Brandon eyepiece), getting pointed in the correct general direction and identifying the stars in the view, and the lack of crosshairs. It presents a reversed field of view; it's not like a right-angle correct image finder.
Atlas selection: Pick your favorite.
Reference material: Use whatever you want.
Personal tips: The Questar, with its compact fork-mounted form, is most comfortable for the observer with objects that aren't high in declination. Nonetheless, I view M81 and M82, at nearly 70 degrees north declination. I use a Tristand. I'm not sure how well one could do this with the Questar on a table. A possible workaround for easier access to the more difficult parts of the sky would be to use the Questar in alt-azimuth configuration on a tripod. You lose the use of R.A./Dec. setting circles and the automatic tracking.
Maybe I haven't said much that helps answer your question. In any case, I definitely enjoy looking at deep sky objects through my Questar.