In-flight rudder and/or aileron trim adjustments are not uncommon for the B737, especially as flap/slat rigging appears to be some kind of black art. I know one particular aircraft that requires left aileron for flaps 5, right aileron for flaps 15, and finally left aileron for flaps 30...
Aileron trim should not be used when the autopilot is engaged, as the autopilot will overpower the trim, which may result in an out of trim condition after autopilot disengagement. However, an out of trim condition will also occur after AP disengagement if the aircraft is, well, out of trim.
The AP can easily mask out-of-trim situations if you don't pay close attention to the exact control wheel position during cruise.
Primary rudder trim technique is to fly the airplane (AP engaged) straight & level in HDG SEL and trim the rudder to the down-side of the control wheel until the wheel is level. Some forward slip is then deemed acceptable. The secondary rudder trim technique is to use rudder-trim until the bank angle is zero. In this case, the airplane may have a rolling tendency when the autopilot is disengaged; aileron trim can then be used to trim out the remaining control wheel forces.
In my experience, the primary technique is usually effective, but rudder trim deflections of up to one unit are not unheard of. This is after all how aircraft were made in the '50s.