Hey Stratos,
I'm not too much into the gear game (like if you buy this plug-in and that synthesizer that'll make you the next best thing) but in this case I actually think a good trustworthy SPL meter or a good omnidirectional mic instead of your phone is the solution. Sometimes hifi stores have these things to rent? I am sure you can find a way to get your hand on something without actually having to buy it just for this purpose!
I recently bought a subwoofer as well that doesn't "fit" in terms of brand to my monitors but I set it up this way (and I am more than happy how it sounds)
First, download the free measuring software called REW (Room Equalizer Wizard) and set it up correctly and feed it with calibration files for your microphone or SPL meter, and audio interface (all explained there)
1. Find the best spot in the room for your sub, there are several methods for this one like putting it in the place where you sit and crawl around and listen for the best response, I think that measuring though is again the most accurate method. Measure just the sub (opened crossover frequency!) and look for the most linear frequency response. Like you did it, place the mic in the sweet spot for measuring - but what I did is to measure some more spots (like at 4 spots around the sweet spot, and then select the 4 graphs and hit average. This gives you more an idea how it actually sounds, because you will probably move your head around a bit while producing)
2. Check phase: just measure both 0° and 180° settings, the one that sounds louder is the right one (level and crossover doesn't matter too much here, I'd set it over 100hz because it might be easier to hear if it gets louder or not. After this set the level that it is about even in the frequency response graph
3. Crossover frequency: again, measure haha! Find out what is most even, although I wouldn't set it too much above 100hz. You probably are going to set it lower anyways since the crossover frequency doesn't affect the output of your sub to the monitors, so therefore is basically just a low pass filter. Just adjust the level while doing this so that the frequency response is as linear as possible.
This is my way of doing it and I hope that it was helpful for you as well!
All the best,
Artless Venture ♢