I'd stick the bridge on the north (top) segment. This side is viewed from both sides, and so it can't host flats. It's unlikely you'll be able to fit many spurs here and still have room for buildings.
The tunnel I suggest putting on a curve. Inside curves are better looking that outside curves because of radius tightness, so I suggest sticking the tunnel on the upper right curve.
i'd make the yard's single end tracks feed from the top. This way they could curve around to the bottom if necessary to get a bit longer. The turntable could go in the triangle of land made behind the ladder, since it's not easily useable for anything else anyway. Plus taht puts it up front where it can be seen.
I like the lefthand wall as it is. I'd make the back track longer though. You can never have a spur too long. besides, the longer the spur, the more cars it holds, the more cars each switch (and money) can handle. This and the little peninsula at left can become town #2, witht he yard and it's backdrop flat industries being town #1.
If your flagstops are passenger flagstops, you can just stick those anyplace there's room for a little shelter that looks cool.
The spur track on the left that goes down, diamonds, and keeps going down. How about duving that at the end and making a longer spur that goes along the bottom leg? Then you could hide the back track here with a large industry that would generate business and divide the layout in two. This way, the yard would be one "end point", and the diamon-spurred town would be the other, with the tunnel and bridge in between. You could even treat it like it's an interchange track with a different railroad, swapping cars from one end to the other, or when you feel more laid back, just clear it and run things in circles.