Kind of hard to give you specific info, since you don't list what type of boat, what brand, etc., but generally:
Most notice a rotten floor by feeling 'soft spots' that give when you walk over them. If you find soft spots in the deck, you have a pretty good chance of having rot below the deck, as boats tend to rot from the hull upwards. That's not always true, but generally, soft spots in the floor are a harbinger of bigger problems.
You often can check for rot in stringers/bulkhead/transom by finding some place where the structure is exposed (e.g., sides of a ski locker are often the stringers; the structure to which the motor mounts are attached on an I/O) and drill into the stringer about 1' from the hull with a 1/4" drill bit. Light colored, dry shavings are good; wet and/or dark shavings indicate problems.
If the shavings are light and dry, fill them with a marine sealant like 3M 5200 or a marine epoxy like Marine-Tex or PC11. If the shavings indicate problems, you have a decision to make.
