Two and Three Story
Be careful changing any dimension that will affect stairs. Redline markups that move stairs on one floor will change the floor opening or landing point on the floor above or below. Exterior walls have a similar problem when creating redlines. Moving exterior walls will almost always change the story above or below. Of course the roof will also be affected when moving exterior walls.
Windows and Doors
Generally a full preliminary set is prepared with floor plans and elevations. This is the time to comment on widows and doors. Occasionally a pre-preliminary is supplied when the square footage and room sizes are questionable. There is no need to comment on doors and windows at this time.
Exterior finishes should be addressed when a full preliminary set is prepared but not a pre-preliminary.
You will not be ready for the redline markup step until after you sketch your plan and the designer publishes the first preliminary set. Please see How to Draw a Simple House Floor Plan
A full preliminary set may contain floor plans, doors, windows, elevations, notes and schedules.
A pre-preliminary set generally contains incomplete floor plans only.
There is a great article about redline markups on the website Life of an Architect.