I set up my Clash Reports 1 vs 1, that way I get a clear picture of where most of the problems lie. If I make sure that all trades are clashed with all others, I will not risk missing any clashes. (In some cases I also have all trades vs all trades per level, just to get an idea of where to start work...)
In those cases where there are lots of clashes (more than 50 generally) between two trades, I start doing narrowed clash tests. For example if Structure vs HVAC results in 3000+ clashes, I would do new clashes for for exampel structural columns vs. HVAC, beams vs HVAC, etc, working my way through the most serious types before addressing less serious (small dimensions through floor or wall).
Within the tests I use the filter function to look at for example large dimensions first, and the column for Level (on the Result tab) to only look at one level of the building at a time.