One building should be used to greet the patients and have all the diagnosis rooms. It doesn't have to be the first building, this building can be located far away from the map entrance, the important thing is to put the receptionist desk in that building. Patients will enter the map, then walk all the way to the receptionist desk, wherever it is located, then find a seat, and wait for a GP's office to be available. I recall when I played I had about two copies of each diagnosis machines and four or five (depending on the number of patients) copies of the GP's offices because patients need to visit the GP's office when they first enter the hospital and then they need to visit it once after every diagnosis machine they have visited until the doctor knows what they have at 100%.

Another building, typically the one nearest to the helipad, should host all of your treatment machines: pharmacy, head popping machine, tongue trimmer, and what not. Again, if you can afford it, having two copies of those machines will guarantee that, should there be an emergency, you will be equipped to deal with that emergency promptly and receive massive cash bonus in return.

Third building should contain the surgery rooms and that big room with the beds for the patients before surgery. If I recall correctly, I don't seem to recall any emergencies that required surgery, and so surgery do not need to be located in the treatment building, it can have a ward all for itself.

As for research and training, you can have a building dedicated for them, but keep your eyes open for opportunities too because you can be very flexible with the research and training room. The diagnosis ward need its own building because there will be a lot of walking in between the diagnosis rooms, and you want to minimize movement in between those rooms. And the treatment ward needs its own building located near the helipad so you can treat patients very quickly when there's an emergency. And the surgery ward needs its own building because again, you want to minimize movement between the room with the beds and the surgery rooms. But research and training can be put anywhere (yeah, I know, it's easier said than done considering how big those rooms needs to be), so be flexible with those. If you cannot fit all your diagnosis or treatment rooms in one building, buy another one near it, put the remaining rooms in there, and if there's enough room, put a training or research room in there too. Similarly, if your diagnosis, treatment or surgery ward are too big, consider squeezing a training or research room in there.

Also, keep in mind that each building will require a restroom and an employee's room. You don't want your doctors to hike across the whole map to reach the employee's room.

If there are still space available in the surgery ward or the training/research area, and those are located nearby the diagnosis and treatment buildings, feel free to squeeze in a couple of treatment or diagnosis rooms that you couldn't fit in the other two buildings.

But yeah, tetrising the buildings so you can fit as many rooms as possible in them is a major challenge in Theme Hospital, I recall having a notepad with quad sheets around so I would designs my buildings before starting a level.

I also recall that around the end of the game, I had an empty space in my treatment building, and whenever there was one of those emergency with eleven or more patients in it, I would build an additional treatment machine in that one empty spot to guarantee I would be able to deal with the emergency, and I would sell it afterward.

Also, a side advantage of having the secretary desk far away from the map entrance means if there's an epidemic alert, you will have extra time to cure the patients because the inspector needs to walk all the way to the secretary desk before it can reward or fine you for an epidemic.