Look for the option 'add new gate'.
Open one of the maps you want to connect, put the cursor on the place you want to arrive when you go into the gate in the other map. Note the coordinates that appear in the brown box at the bottom on a piece of paper.
Then open the other map, go to the tab that has the gate option on it, and enter the coordinates you noted down. Then click on the button add new gate, and place the gate.
Do the same thing the other way round, then you're done.