The equations of motion themselves shouldn't vary really; what you're going to find varying wildly are the forces and moments input into those. The aerodynamic components are going to become pretty negligible pretty quickly - rule of thumb, aerodynamic forces beome negligible at 50-60 knots for a conventional aircraft - so you'll need to have a good understanding of RCS and engine forces at lower speeds.
(I'm assuming you're approaching this from a generic equations of motion model, plus models for the input forces and moments in each axis; that's my guess at the safest way to handle something like VSTOL, certainly. Trying to use some kind of approximation that works for a regular aircraft then blending in some kind of low speed EoM is asking for trouble, IMO)