Like said, each kit is different and just because the 1:1 prototype can be lowered a certain way is no guarantee a given kit of the same car can be lowered prototypically. So with each kit certain decisions have to be made and certain concessions to the reality have to be dealt with. If you dont really care how things look underneath you can glue the top of the tires to the bottom of the fender well and even cut off the top of the tire so it will tuck up in there better. If you are more picky how it looks under there, then, as suggested, perhaps you can liberated the spindle from the control arms and raise it up, effectively lowering the car. Other times its fairly simple to mod the suspension just as prototypically you could to get it lower to the ground. Sometimes you do a combination of things and of course things like shock absorber length come into play. One problem i often run into is the suspension lowering is easy, its the inner fender wells or inner lip of the fender opening that are the problem. I often grind away clearance for a radical lowering job, which is what i most prefer. Sometimes lower profile tires or smaller wheels will help if appropriate to the car in question.
Most often i choose the path of least resistance but that is governed by whether i want the undercarriage to look realistic or not...if its a slammer then i just slam it but if i want to show the underneath then more care is needed. Sometimes its as easy as reversing the spindles either side to side or upside down, if the wheel mounting spindle is higher one way than the other.
In the front though, and many times in the back too, some thought will have to be given to what to do with the tie rod and/or control arms as they might not fit into the space allotted to them when lowered.