Which order to apply room correction tools?

That's nice. There is by the way no such thing as time alignment with subs. But being impatient, carry on.

The best method is speaker placement. First being to find the best location for response, then after that to get them absolutely precisely symmetrically equidistant for imaging.   

With three subs they should be asymmetrically distributed around the room so that each sub as well as your mains are different distances from the corners of the room. This alone will achieve a very smooth low frequency response. Set the sub levels and you are about 90% of the way there. 

From this point on if you think anything is a matter of pushing a DSP button, good luck! No electronic room correction does anything even close to what it says. It does nothing for example to correct the room. Everything it does is to the signal. No getting around this.  

The fact of the matter with rooms is they are all so different and particular there really is no solution other than to sit and listen, walk around and listen, clap your hands and listen. In other words listen. Don't take my word for it. Mike Lavigne has the best room I have ever been in, and he paid big for it, some of the best acoustics guys on the planet, and even with all of that why is Mike's room so doggone good? Because he listens! He has made all kinds of improvements to his room, and the better it got the more he heard and by listening closely has been able to continue to find areas of improvement.

Your room is no different. The fundamental process is no different. Learn, look, listen. Try stuff, hear what it does. DSP is a crutch. Toss it. Get some Owens Corning acoustic panels, or GIK if you want to spend more for the same thing. Get some Synergistic HFT. Use these things. Move them around. Listen. Learn from your mistakes. Listen. Find a way to make it even better. That is the order of the process.