If one wants to measure the speaker alone without the room, you limit the listening time on the mic in the software. So the software sends out an accoustic signal and you can set in milliseconds how long after that it's allowed to measure. In the impulse response window in REW you see the pulse from the speaker, a quiet part, and then new ripples. The new ripples are the echo and should be cut out by adjusting the listening window. Then you measure only the speaker from ca above 800Hz and upwards. Then you get a baseline for further tweaks. Its an awesome tool and lets you understand whats going on much better. Going only by ear is almost impossible/very slow compared an spl graph and waterplots. I highly recommed you start with some guides to get started with eiter REW or ARTA. Its going to help you achive the sound you want much faster
There is some decent REW info on Youtube which is enough to get you started!