I am pretty outspoken on this issue. Probably because next to being a long time DJ I am also a sound engineer. 3-band EQ on mixers (or any other gear), especially those with fixed center frequencies and bandwidth is usable primarily for fine tuning some particular things in a (mic) channel. This type of EQ is singularly unsuited for room EQ, which is the only reason a DJ should use it since you have full channel EQ for fine-tuning and effect purposes on your controller already.
What I have seen happen if you give DJs access to EQ on a PA mixer, is that things get turned up (especially) bass because it becomes even louder. The end result is never an improvement.
So my basic message is, if you don’t have the skills and/or knowledge and you don’t have the gear, don’t touch the acoustics.
With the EQ out of picture and fader riding not an issue (once you set the 0dB gain path throughout, you don’t really have to touch the PA Mixer volume level of your controller input anymore. Thus, it really doesn’t make a difference if you use the TRS (are you sure, often line inputs on lower and mid-range mixers are simple TR, so unbalanced!) inputs or the RCA.
Clearly if they are truly balanced TRS connections and you controller has balanced Jack/XLR outputs and the PA mixer is not within a few feet of your controller, then the balanced route would be best. Otherwise just hook up to the aux from your rca outputs from your controller.
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