I've done several of these. You can't just copy and paste your map into a QR converter and expect a good result.
First off, start with an all-green canvas. It can be light green, dark green, whatever green you like. Then pick out a blue for water and a sandy yellow for the beach. Pink for Retail, grey for the police station and cobble stone, brown for Brewster, purple for the town hall, and a darker green for the town tree.
My tips:
1) Start with the ocean. It gives you a good outline for 2 of the four sides. I typically make the ocean 2 pixels wide.
2) Do the beach outline. If you have a straight beach, then do 1 pixel all the way down. If you have some bumps or crevasses that make your beach look like it's a bit bigger, do those in 2-3 pixels.
3) Based on your beach and ocean placement, determine how far down or across the river mouth should be. If it's about 2/3 of the way down on your map, make 1 pixel across the beach to where the river should be.
4) Map the river. I like to use the lake as a focal point. If it's about half way across the map and 1/3 down, then try to do that with your canvas map. The river should be a 3x3 square with 1 pixel in the middle of each side. You can then adjust it based on where the river connects to the lake.
5) Map the ponds. Try your best to reflect the shape of the ponds. Ponds are relatively small, most being only 3-5 pixels large.
6) With your entire landscape mapped out, you can now fill in where the landmarks are. I like to make my Retail, Police, and Brewster 3x3 with the bottom middle removed (so like a fat upside down U shape). The town hall is 4x3 with the two bottom middle pieces removed, but filled in with grey and grey around it (for the cobblestone). I mean, you could make them any shape you want, but those are my preferred dimensions.
This is an example of what I've done for someone:
http://i.imgur.com/cT3Uiwp.jpg