What is causing the flooding? I'm guessing it's not a typical plumbing problem (broken pipe) if it is a recurring one. I would address that before I lifted a finger to renovate.
I would not put down carpet, of any kind, if you can expect more water. There is an engineered flooring that is designed to get wet. It is a solid urethane with an anti-microbial, cork backing. It's an easy to install, interlocking, floating floor system. That said, preventing future flooding is the answer first. I would spend my $$$ on fixing the problem before I spent a penny renovating.
Depending on were the water is coming from their are plenty of low costs fixes to mitigate the problem. It doesn't always have to be an in-basement, trenched, sump system. I've alleviated some pretty severe problems with Ditch Witch from Nu Way and $100 worth of Corex. I've also used an epoxy based, hydrostatic paint to fix more minor basement issues. Doing it yourself will save you about 5X the $ from calling a basement service.
