Yeah... I wouldn't use bass boost at all. You're essentially telling the amp to make bass that isn't there and it can lead to clipping.
Sounds like those installers didn't really know their ****. Who knows. None of the shops I've ever been around would ever do that, but it could have just been those installers. I've some do some pretty stupid stuff. The shop was a great shop, just that one idiot.
I'll be honest, I do most of my tuning by ear for distortion. You can tell when a sub is being run too hard or the amp is clipping. Then I tend to bump it down a bit to where they can't possibly clip or be driven to hard for customers. If they know what they're doing, they can adjust as needed, otherwise they tend to keepsl hands off.
Its up to you, I would reset the gains myself personally, but I'm really comfortable with getting it right or dealing the consequences if I don't.
