Well, you could but it wouldn't make sense IMO. You have to understand the fundamentals first. It's akin to slapping in 1000cc injectors and expecting instant HP gains.
Just do a little research on what water does and what meth does and then ask yourself what you want out of it. That's really the starting point. Do you want a denser charge for more power or do you want a cooler charge to mitigate timing retardation under boost (prevent detonation). Are you just wanting to run low octane fuel in your FI'd motor?
What size nozzle(s) are you going to run and where? Pre SC or directly into the intake mani? I don't have any answers for you, just saying that a good tune in an FI'd system is already sophistacted balance of variables. Then you add water/meth injection along with its computer (probably just MAF based too) and that's a whole other set of variables to calculate.
I'm not trying to sound discouraging because water/meth injection is very cool, no pun intended, when it's done right. Systems have evolved pretty well nowadays but it's still not a plug-n-play proposition. I guess this is the verbose way of answering your original question. Yes, you will most definitely need to tune for it but you must first understand what it is and decide which goal you want from the start.
BTW, slightly off topic but related: I don't see much talk about knock lights in all these FI'd systems but I think they're essential if your goal is to eliminate detonation to begin with.
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