Designing from two positions
A functional appliance is unusual in that its geometry is defined by a position the patient has to be placed in. The functional bite you register, forward and open relative to the habitual occlusion, is what the appliance has to hold. The design therefore articulates the arches twice: once in habitual occlusion, to record the starting relationship and check clearance, and once in your functional bite, to build the blocks that will hold it.
The registration is used as supplied. The amount of advancement and the vertical opening are read from your bite, not constructed from a formula, because they are clinical decisions that depend on the patient's range and the protocol you follow. The design measures both and states them, so that if the registration does not match your prescription the discrepancy is visible before the appliance is made.
Where the plan calls for stepwise advancement rather than a single registration, the design can carry the successive positions as versions, each built from its own registration, so that the reactivated appliance is planned rather than modified by feel.