It is always great fun and at the same time quite painful to tune subs, especially in a stereo setup, more so if your room gets in the way.
Before you start, you will have to look at subwoofer company recommendation for the model, to go with line level (RCA/phono) output or speaker level output from your source.
Some companies recommend speaker level while others RCA level (in some subs there will be only one choice, so the connection is then straightforward)
If both inputs are available and no specific recommendation is provided, then try both option and see which sounds the best.
In my Wharfedale sub, RCA input sounds the best and is also the one recommended as per its manual.
The approach I normally take when tuning with ears:
Start by putting the sub in the center of the 2 speakers and draw it out by around 18 to 24 inches from the rear wall.
Sit right in front of the sub and play a track with good amount of bass and at your normal listening level, and first set the crossover at close to the roll-off point of the bookshelves.
Then increase the db level (the volume pot) on the sub till you can start to localize the bass note to the sub.
Play around with the phase. Stick to the changed phase if the bass remains tight but loses localization. Go back to the original phase of bass becomes lose and hollow.
Next, go down a point on the crossover and observe. If the bass loses localization, again raise the db level till the localization again starts.
Play with the phase again and stick to one that sounds tight.
Now push back the volume till it feels as if the sub notes are coming out of the bookshelves and not from the sub (you will start to get a sense of height and the sub notes moving further back when you sit right in front of it).
Now move back to you normal listening position and listen. Ask someone else to increase the volume on the sub very very lightly so that is sounds the best without impeding other frequencies.
Switch the sub on and off to listen to its presence and absence.
If you feel the right amount bass with its presence and not hear it off the sub, you are close to its being coherent with the main speakers.
Now again listen at both low and high volumes to ensure that the impact is uniform. If not play around very lightly with the sub volume control to get it just right.
There is no harm is vocals getting weight as long it does not hamper the openness and warmth (should not sound hollowed out).
Play more well-recorded tracks of different genres to ensure what you listen is to your satisfaction.
However if you have the hardware tools and understanding and the interpretation of the software tools, then you can do all this more easily with multiple room placement checks.