Select "New" from the menu after launching the toolchain. Input all the data it asks. After that, a window will launch with your tileset on it, and instructions. Navigate the cursor to the tile it asks you to find and press Space on it. Finish and it will naturally quit. If you make a mistake, press Enter before you complete the map-pack, and try again with Map-Pack Wizard -> Edit Tile Equates.
To create a map, load your map-pack then select Map Creator. You can load an existing map from your map-pack or start a new one. A new one will load all blank.
Place down tiles using Interact (default Space), and maneuver using Up/Down/Left/Right (default WASD). Press Q and E to switch the tile you're using, or - and =, if Q or E are already mapped to another action. Switch between placing tiles and objects using Attack (default Left Shift). Objects are ordered as follows:
Maps are loaded in like such: first map -> top-most left-most map, second -> top-most, one right of left-most map, etc., wrapping around every 10. Map #10 is the right-most map of the first row, and #11 is left-most map of the next row.
The tileset should be made of 48x48 tiles, and it should be formatted with rows of 8 tiles and columns of 16, so the size of the tileset image is 768 x 384 px. Map nubmers in scripts are referred to as their line number, minus 1. This is also called the map ID. For example, the map on line 1 would be map ID 0.
Save your map by pressing Menu (default Escape), closing the window, or Enter/Return. Copy the data that's outputted to the console or output/map.txt to your map file on the line number you want it to appear. Use this tool to convert map coordinates in (x,y) to a line number.
A script is a line of data that corresponds to a certain action. This allows you to customize your experience with text boxes, bosses, teleporting, etc.
You can learn more on the scripts info page.
When you first created your map-pack, you defined several things such as where to find your files, where you want the player to initially spawn, and what tiles map to what objects. During the development of your map-pack, some of these things will likely change.