In terms of the machine design process it is fairly iterative and you need to go around the loop many times as every choice has a knock on effect that ripples through the design.

Assuming you are building a fairly standard machine with moving gantry and raised X axis then I'd suggest you draw the spindle with your favourite tool in the collet and place the tip about 150mm above the top of the bed plane.

Draw the Z axis plate that holds the spindle and make it say 300-350 mm tall by 150 wide. The bottom of the plate should not be lower than the main spindle body. Add the Z rails to the back of this plate making them at least 300 mm long and ideally matching the height of the Z plate.

Add the lower carriages to the Z rail placing them no lower than the main body of the spindle. In the CAD program slide the Z axis (spindle, Z plate and Z rail) down until the tool hits the bed plane. The lower carraiges should remain in place.

Add the upper Z carraiges near the top of the rail, leaving 10mm or so if you want a bit spare to face the bed.

Draw the Y axis plate which hold the Z carraiges on the front side. On the rear of this plate add the Y carraiges making sure they do not clash with the Z carraiges and that it can be assembled!

The Y rails can then be drawn to fit the Y carraiges and the gantry drawn.

Add horizontal plates on the ends of the gantry and fit the X carraiges to the underside. This dictates the X rails position.

Draw the frames to hold the X rails and then add vertical supports under these frame sides to connect down to the bed frame.

Add the steppers, ballscrews, ballnuts, and ballscrew mounts and the fun starts. Things get tweaked and moved to get it to work. I would say this bit takes the most time so hang in there.

Finally plenty of advice on hand on this forum to guide you. Best of luck!