No way to avoid them, just how you aproach them. Mostly takes experience as to different heights and lengths. Your speed needs to be different, or your angle of approach. Nothing wrong with just getting to an idle and ridding it out.
Do you have a jetovator or similar setup, Put your nose up to soften the blow.
Along the river and in some of the sloughs in my flattie;
Ive found that if your coming up on a boat throwing a big wake move to the side where the wake has not spread the width of the lane and pass there. or where it is smallest.
With an oncoming boat that has already spread a wake the full width of the lane your gonna have to again run to the side that has the shortest height and probably close to shore to get over it.
I will usually drop my speed immediately before to 'break' the wake and throttle on over it. seems the flatbottoms are pretty good for smashing them down. But yes always at a severe angle to the wake or it becomes a RAMP!...