Haven't personally been through this saga, but a friend of the family owns a construction company that has done several for large corporations. It's not unlike building your house. You've gotta figure out: (1) What you have to have (office space, hangar floor space to include any future fleet growth, passenger lobby needs, galley space, yada yada yada...), what you'd like to have, and what's nice to have but you can live without to come in under budget.
EVERYONE, from the top boss on down through yourself and fellow pilots need to be involved because you'll be hearing about all the things you should've done but didn't for years to come. Don't forget the needs of the company's customers that may be coming through as this is most often their first impression of the company on a corporate visit.
My best suggestion is to go with someone who's done quite a few from start to finish and their going to guide you through the process. Take the opportunity to drop in on a few hangars while on the road to get ideas from others.
Good luck!