Damonjynx,
Doorways, Traps, Hazards, Treasure, Themes , Monsters, and other interior additions that populate a dungeon might be hard to do with tiles. Each transition between one random room or passage has a chance of having one of several different types of doors, possibly trapped, if my memory is right (don't have my book on me ATM). This section of the random dungeon generation process might cause quite a bit more work depending on how you plan on representing it on your tiles. If you make each door type a separate tile you would need to figure out how it can seamlessly be implemented without throwing off your grid. How you envision your tiles being used greatly changes what options you can have, or so I think.
You could take a look at what WOTC has done with their D&D board games for reference, but that might warrant a cease and desist letter if you plan on profiting from it in any way. If it were me, I would pull up Microsoft Office/Open Office and using an Excel document with columns and rows of identical size (thus creating a grid that is theoretically 1mil x 16000) I would insert your images and snap them to the grid. If done this way, doors and other interior stuffs can be placed over the hall, room, etc. image.
You have quite a lot of options at this point in your project, and no matter which way you go with it I feel it will be quite grand. Keep up the great work!