Not an expert here and did not stay at a Holiday In Express either.....
It is very difficult to tell you precisely what to do. Only suggestions can be given. If you look at most of the RF builds you will see they all vary a bit and are custom to the builders or customers taste.
A simple description of a RF smoker is you have a horizontal cook chamber with a fire box to one side. The smoke and heat pass under a metal plate that runs about 85% the length of the cook chamber. The smoke and heat rise into the chamber and then travel to the opposite end where there is a stack at the fire box end where the smoke and heat exit the chamber. The air flow is the key to this style of smoker to work properly.
Not sure if allowed, but here is a link that should help with some of your design:
http://www.feldoncentral.com/bbqcalculator.html
You will be able to play with the numbers on your design to get an accurate dimensions for the stack, fire box, openings, etc.......
As stated earlier it is usually easier on the build if your fire box is the same width as your RF plate. This way they match up better for the weld seems. To determine the width of your RF plate and fire box will be determined by the width of your tank at the point where they will sit. The calculator will help with that. I have seen the placement of the RF plate as close as 4" to 6" under your bottom rack.
For how far to inset your fire box. That really is up to you and what you want. Most if it is a dome end they will inset to the weld seem. Most if it a flat cut off end will not in set it.
Stack placement is at the firebox end. The length is determined by the diameter of the tube, you are not limited to round square will work, just need the correct volume for the draft. Wider is better for less resistance of the air flow.
If you are able too, go a little bigger on your fire box, vent opening and stack size. This will give you more wiggle room for the numbers.
Jeramy