There are several ways to queue EM Converters in SplinterFaction, and that variety confuses people. So here are all three, side by side, and the reason the most familiar method isn't one of them.
The problem with area-mex
A lot of SpringCoil players (my shorthand for anyone who was around for the Spring RTS engine and is now here for Recoil) are used to a widget called automex. The idea is simple: select a builder, click automex, drag a circle, let go, and every resource location inside the circle gets queued.
It's very fast. It also takes away something important: the choice of which path your builder takes. If the edge of your circle brushes a risky area, the queue will sometimes send your builder there before the safe spots. That happens often enough that I consider it a real problem. A cheap builder walking into enemy fire because a widget chose the order is exactly the kind of thing SplinterFaction's controls are meant to prevent.
Three ways that keep you in control
1. Select the converter, then shift-click
The simplest method. Select a builder, select the EM Converter, hold Shift, and click near each resource location in the order you want them built. A yellow line snaps to whichever spot is closest to your cursor, so you don't need to be remotely accurate.
2. Shift + right-click
Borrowed from Beyond All Reason. Select a builder, hold Shift, and right-click directly on resource locations. No need to pick the converter from the build menu first.
3. Right-click and drag: connect the dots
This is the replacement for automex. Select a builder, right-click on a resource location, and drag a line from each one to the next, connect-the-dots style. You only need to be reasonably close. It takes a moment longer than area-mex, but it's far more controllable: the line you draw is the route your builder walks.
Here is an example of how it's done:
Which should you use? Whichever is fastest for your hands. Methods 1 and 2 are best for a couple of spots; method 3 shines when you're claiming a whole field and want to sweep it safe-side first.