Some cleaners are just very alkaline, so it should not effect the wheel wells, but I'd cover the tires/wheels with towels.
As long as it's not some acidic cleaner, I see no problem even with vinyl wheel wells as the engine compartment has similar vinyl/plastic in it.
After you get them clean, I found that Megs EngineKote works well in protecting them the longest. It's really some type of floor wax... smell it and you'll see what I mean! Dried hard!
Found it spatters in the engine bay, so I do not use it in there anymore, even if I used a very fine high-volume sprayer it still spattered into small white globs. Mostly caused by previous dressings still on the area, so a very clean bay it may not splatter as much. So now that's why I now just use it for undercar work!
Regards,
Deanski