So the question is would I be able to use ST to keep all frequencies balanced from one tune to another?
Yes, with proper multiband compressor settings, this is possible. The configuration file I sent you applies extreme compression to 16 bands across 2 multibands. This is usually not recommended. Try some of the presets included with the software for a much more professional sound.
Initial question is my DJ Software which is what I use most of the times has a built in Compressor Limiter which works well to control the overall volume level, should I disable it or leave as is please?
You would probably want to disable the effects on your DJ software and allow Stereo Tool to handle any audio processing that might be done by the software. I'm guessing Stereo Tool will likely have a better auto-gain control, compressor, and limiter than the ones built into the DJ software (once properly configured).
Also, I am wondering if maybe first running all of the files on my HDD through a processor will help and if yes, any recommended processor for this purpose please?
The answer to this question is that you would probably want to keep the original files in their original forms, rather than using something to process them all. This is because Stereo Tool is always being updated, refined, and new features are often included with each update.
However if you want to do this anyway (for putting processed copies onto your phone or whatever) you should use WatchCat, found on the Stereo Tool download page. You can import a .STS (Stereo Tool processing configuration file) and apply processing to copies of your tracks.