Okay to change crossover setting after using Yamaha Auto Setup?

[ridergroov1]

Hi folks. I can't remember where I read this but I'm thinking I read that it is not okay to change the crossover setting after I run the Yamaha YPAO setup routine with the mic. Something about it negating the Parametric EQ that it sets up. When I did this it set my crossover to 90 which was okay but now I'm noticing that I can tell that my sub is on the left side which is somewhat distracting. I talked to someone at SVS and they suggested maybe that the crossover is set to high at 90 and suggested putting it to 60. Is this okay to change after running the YPAO setup? I was hoping to use the PEQ it sets up but I don't want things off balance with that by changing the crossover after setup. Thanks.