You do it much the same way as the DX7 by using the menu for setting the flap position. I use the JR9503 and actually can control the servo speed, plus reassign to 1 of 2 analog settings to have unlimited positions. But with the switch, you can set the trims to exactly where you want them.
Don't know about the Eagle Tree data logger, but I bought an Eagle Tree stand alone altimeter for my son's science project last week. It works great! I'll be peicing together the logger, airspeed indicater, etc. over the next few months. Seems like they are quality products!