There are several ways to account for deformed shaped in staged construction and for placing newly added joints into their deformed position.
Modify Undeformed Geometry
The most useful approach in many cases is to start with coordinates representing the desired final deflected shape of the structure. After running the staged-construction analysis, use the command Analyze > Modify Undeformed Geometry to change the joint coordinates so that the deflected shape at the end of the staged construction case matches the originally specified geometry. Iterate a few times until the coordinates converge to the desired shape.
This approach automatically gives you the desired location of joint at the time it is added to the structure, and the deflected shape is meaningful. It also has the benefit of calculating camber for you.
The Concept of "Ghost Structure"
(1) Define two Named Property Sets of type Frame (or Shell) Modifiers using "Define > Name Property Sets" menu command. Let’s call the first set "Ghost" and the second set "Full". In named property set "Ghost", set all stiffness modifiers to a small value, say 1.0e-4, and the mass and weight modifiers to zero. In named property set "Full", set all modifiers to 1.0.
(2) In the first construction stage: Add the whole structure. Apply named property set "Full" to those objects that are present at the start and load them. Apply named property set "Ghost" to the rest of the structure.
(3) In subsequent stages, Apply named property set "Full" to the added elements and load them.
At each stage, the entire structure deflects, but only the objects set to "Full" contribute significant stiffness. This results in joints being activated in a deformed location that may be meaningful. Note that this approach can be modified as needed by considering partial or multiple ghost structures.
The same approach can be used by changing sections instead of changing modifiers. For example, you could use a plywood section for deck shells, and later change them to concrete slab sections.
Both options are discussed in the CSI Analysis Reference Manual, chapter "Nonlinear Static Analysis".
Manually Modifying Joint Coordinates
For unusual cases, you can manually get the initial joint coordinates by running multiple analyses.
Start with a model having preliminary joint coordinates, and run the first stage of construction. Modify the coordinates of the joints that will be added in the second stage so that they have the correct location with respect to the deflected shape of the first stage. Re-run the analysis for two stages, locate the joints for the third stage, and continue this process recursively until all joints in the model have been located.