That is correct, assuming you use sub1 for the left sub, then you would connect the left tower with sub1 and right tower to sub2. Also, for best result you would have to re-run Audyssey so that it would time aligned sub1 and sub2 again and then EQ them together. You see that's why the so called 7.2.4 is a misnomer, it doesn't matter how many subs and/or subouts you have, it is really 7.1.4 because there is only one single discrete subwoofer channel. A true sub1 and sub2 such as Denon/Marantz is only two discrete channel during the time aligning process done by Sub EQ HT.
Please make sure you use the App and save the file/curve in a different name so you know which is which without having to re-run Audyssey again.
Also, the AVR-X4700H supposedly can save two files/curve/settings(only if I understand the feature correctly) on the AVR so it should be easy to compare without having to re-send the curve every time.