... the specifications just say "wireless multi-flash support". What does that mean?

It's obscure, but basically what that spec means is that the M6 can only do Canon's wireless flash systems (both radio and "smart" optical) via the flash hotshoe and camera menus, but not with the pop-up flash. You have no built-in "master" unit to trigger an off-camera flash, you need additional external flash units (i.e., "multiple flash units": one on camera to act as master, and one or more off-camera flashes to act as slaves).

As far as I understand theres two different modes - one is infrared/flash control where the built-in flash controls other flashes. Is this visible to the naked eye?

Actually it's near-infrared, and the signaling is still in the visible spectrum. :) But you probably won't see it, as it's very quick. And as I said above, the M6's pop-up flash does not have this capability. You need a higher-end dRebel or prosumer dSLR body to have this function in the pop-up flash. The EOS M, SL, and lower-end (XXXXD) dRebel bodies do not have this capability. To use this system, you'd need a "smart" optical master unit on the hotshoe, such as an ST-E2, or a 580EXII (see: Is there a Canon equivalent of the Nikon CLS?)

Does this actually fire the [popup] flash at the time of the photo (enough to light)? ... Can I have the 'master flash' (even if its not the built in one) NOT light the scene, but only signal to other flashes?

If your camera had the Canon "smart" wireless master capability, you can set the "master" unit not to fire at the time of the main burst. The flash, however, will actually fire (as the signal to the remotes to fire), only at a low enough power setting that, at non-macro subject distances, its light should not appear in the image. But your camera doesn't have this capability.

The only optical slaving system you can use with the M6's popup flash is a "dumb" optical system. This is often called S1/S2 mode on some 3rd party flashes (Canon's own speedlites cannot do this). This type of mode is manual only (can only fire the flash, no settings controls), and simply uses a sensor on the flash to tell the flash to fire when it "sees" another flash burst. S1 will fire on the first burst sensed; S2 on the second burst (thereby skipping a TTL metering pre-flash). If you are using one of these modes, then the pop-up flash will have to fire brightly enough to set off the optical slave, and that may register in the image.

The second one is radio controlled. This needs a transmitter, right?

Yes. This is true of any radio flash triggering system, not just Canon's RT system (e.g., Godox's X, Nissin's Air, Cactus's V6, Yongnuo's YN-560/622/RT, or Phottix's Ares triggers, etc. etc). You need a transmitter unit on the hotshoe of the camera to act as a master, as well as receivers either attached to or built-into the off-camera "slave" flashes.

See also:

• What features should one look for when selecting a flash?
• What should I look for in a wireless flash trigger for a home studio?