Jake, it sounds like the motor coil wiring on the blower that doesn't work may be damaged or has been disconnected.
Regarding the one that is still running. The automatic fan control is located on the bottom of the blower assembly. The fan control is a nonadjustable, automatic type. The fan control will require between 3 and 7 minutes of main burner operation before the fan control "closes" and activates the blower. The blower will continue to run between 3 and 7 minutes after the main burner shuts off, before the fan control "opens" and deactivates the blower. In which case, if it continues to run and run and run, the fan control switch (part # R-2503) may have failed and will need to be replaced. You can order the part from Empire Comfort Systems Tech Service 800-851-3153. Have the Model Number, Serial Number of the heater handy, as well a the Part Number. when you call.
To help you further, I have included a link to the Owner's Manual for that model wall heater. You can download and print it for future reference.http://www.empirezoneheat.com/assets//EHS/manuals/GWT-%2825,35%29_Manual.pdf
I hope this helped you troubleshoot and solve the problem. Please let me know. Thanks.