There are a lot of parts into the game where i just dont know what to do with the die. For example, when I have to roll a 3+ to cross a bridge, how many dice is it when it's not a might or speed or sanity or knowledge roll?
There are a few separate rolls that aren't based on a trait. Usually, if there's no trait to check it'll tell you how many dice to use. This includes events such as the granny on the telephone and rooms such as the mystic elevator (both 2 dice, from memory).
One common type of roll that doesn't use a trait is the haunt roll, which you roll after each omen card is drawn. As detailed in the general rules, a haunt roll is always 6 dice, and succeeds (doesn't trigger the haunt) if the result is at least the number of omen cards drawn so far. Since you can roll up to 12 on 6 dice, there are 13 omen cards (and omen room tiles) to guarantee that a haunt will always happen eventually.