My character was bitten by a Dire Rat and through accidental meta-gaming reasons, I know he's incubating Filth Fever. I want to ask the Paladin in our party to remove it before it can affect my stats, however, I don't really know if my character would know he's ill before the stat damage occurs. Is there any ruling for this?
When a character is injured by a contaminated attack, touches an item smeared with diseased matter, or consumes disease-tainted food or drink, he must make an immediate Fortitude saving throw. If he succeeds, the disease has no effect—his immune system fought off the infection. If he fails, he takes damage after an incubation period. Once per day afterward, he must make a successful Fortitude saving throw to avoid repeated damage. Two successful saving throws in a row indicate that he has fought off the disease and recovers, taking no more damage.
These Fortitude saving throws can be rolled secretly so that the player doesn’t know whether the disease has taken hold.
Emphasis mine, that last line only makes sense if the character doesn't know.
But, of course, even if the character doesn't know that he's incubating a disease for sure, he could suspect it. Dire Rats are animals, if the character (or any member of the party that witnessed the attack) has ranks in the skill Knowledge (Nature), he could know that these creatures have an infectious bite, and that you could have been affected, and suggest healing magic just as a preventive measure.