If you have experience with DMR and D-Star, you will find using System Fusion much easier.
1. Program your callsign into the radio (which it asks you to do on initial power up).
2. Dial up the frequency of your local System Fusion repeater on the A band (top display). If the repeater is using the standard repeater offset, the proper offset should be set automatically.
3. Press the Dx button until the A band display reads "DN" with a bar flashing above it.
4. Key the PTT and talk.
Assuming your local repeater is set for Automatic Mode Switching (AMS) in and out, the repeater will hear your digital transmission and repeat your signal in digital. If someone responds to your call in digital mode, your radio will hear them and decode the audio from the digital signal. If someone responds to your call in analog mode, your radio will switch to analog (the flashing bar above the mode indication means your radio is set for AMS). Since the other station is in analog, you will probably have to respond to them in analog which means you may need to set the proper CTCSS tone or DCS code to access the repeater in analog. Unfortunately, this is a bit of a pain on the Yaesu radios, but it can be done through the user interface without having to resort to programming software.
Granted, there is more to using the FTM-400 than the four steps I listed, but that's the gist of using a System Fusion radio on a System Fusion repeater in digital mode.