What instruments and pickups can I plug into my Relay transmitter?
Relay digital wireless systems basically just replace your instrument cable so basically you can plug anything into the transmitter that you could have plugged into your amp (as long as you don't exceed an input level of 6V p-p at the input).
Instrument with piezo pickup - If you are currently happy with the sound you get from plugging from your instrument into your amp, then your rig will work just fine substituting Relay for your cable. The input of the Relay transmitter has a very high input impedance (1.3 Mohm) so as not to load down your instrument. This is equal to or even higher than most preamps specifically intended for piezo pickups.
Stereo pickups with Y-Cord - Could also be standard pickups combined with a bridge saddle pickup. Again, if you are happy with the sound you get using this configuration then Relay will not get in the way of your sound. Or you could run each pickup to it's own individual Relay system which could then be split into stereo.
Active instruments w/ preamps - If your instrument has an active preamp and is powered with a single 9v battery you will have no problems using Relay. If you have a double 9v preamp it is theoritically possible to clip the input of the transmitter but unlikely in the real world. Should this actually happen you can remedy it by backing off a bit on the master volume control, adding a pad to the cable or removing one of the batteries. The extra headroom offered by these systems is only a benefit if it fits in with the system gain structure (unless you are using it to purposly clip the input of your amp). Remember, unused headroom is wasted.
Where should I plug Relay into my chain?
Relay replaces the cable from your instrument to wherever the other end of that cable was plugged into. Plug your instrument into the transmitter and plug the output from the receiver into wherever that cable was before. Generally speaking, you are un-tethering yourself from the first piece in your chain. You don't have to worry about gain or level matching as Relay is a "unity" device. That means you get the same level (voltage) at the output jack of the receiver as you are getting from the output of your instrument. Nothing changes ... Relay's output level is neither louder nor softer than the original.
The output from the "tuner" out is exactly the same as the main output in level and impedance. Only difference is the pressing the "mute" button on a G50/90 transmitter shuts off the main out but leaves the tuner output active. The XLR and 1/4" outputs on the G90 are also identical and are provided to give the user more versitility in connecting to other gear.
What IS different?
Depending on how you've set the cable modeling, you could be sending a lot more "highs" into your system than ever before. This could result in more apparent noise or hiss. It would be the same as if you had connected your instrument into your system with a 1-foot cable (which is pretty difficult to do unless you are a contortionist guitarist!). Adjusting to the proper cable model should remedy this situation. On the other hand, if you are using an acoustic guitar leaving the model off will sound like the freshest set of strings you've ever played.