For any project that will change a type certificated product, the first thing is to define the outcome of the project completely. In the sample case, the seating arrangement is the proposed project. Once the scope is defined, identify everything that will be touched by those changes. Next go to Order 8900.1 Volume 4 Chapter 9 figure 4-67 and follow the flow chart to determine if you will need an STC, or if the project could be done with a Field Approval. Next go to the same document and look at figure 4-68 and use this table to determine what level of support will be needed in developing the proposed modification. The next thing would be to have a meeting with the appropriate FAA office for the project. If it can be done via Field Approval, then your FSDO Airworthiness Inspector is the go to guy. If you need an STC, then you will have to go the an Aircraft Certification Office. In either case, the FAA will identify all the relevent FARs that you will have to show compliance with in order to gain approval. Since the case at hand is a CAR 3 airplane, that is the Certification Basis and for the most part, those are the regulations you will be required to comply with. In some cases, you may be asked to comply with the current FAR 23 regulations, but only for certain items.
If it is determined that it can be done by Field Approval, the process is much easier, but may still require hiring a DER to work the structures and systems issues.
Once you know what you will need to comply with you can start the detail design, or thow out the idea based on cost or feasability. With the detail design finished, build the prototype (if its a one time, the prototype is the finished product) and if the modification changes limitations, aerodynamics, or systems, you may be required to show compliance with the FARs by flight testing. If the design is really radical, you may even have to go Research and Development to prove the design will even work. A Manufacturing DAR is required to issue an Experimental Show Compliance airworthiness certificate for you to perform the tests required (with a formal test plan). Either a Manufacturing or Maintenance DAR can issue an Experimental R&D certificate (consistant with their letter of authorization). When the test plan is complete and documented, that package would be sent to the ACO, and they would issue the STC. This process can take months, and the aircraft can not be returned to standard category unless you have the STC in hand, or you remove the modification and return the airplane to the original configuration. To go back to Standard either with the STC, or modified back to original, you need a Maintenance DAR. Not an easy or inexpensive process, but do able.
All in all, you may have to hire a couple different DERs based on their areas of authorization, and a couple different DARs to get the job done.
http://fsims.faa.gov/PICResults.aspx?mode=EBookContents is the link for Order 8900.1
Hope this helps for anyone that is planning on making mods to their airplane.
David Schober DAR-T