There are two different kinds of crusades -

Player started.

Non-player started.

To initiate a crusade, you must have good pope-o-meter standing (through building churches, high religious values, obeying the pope etc), and open up your diplomacy/papal standing scroll. Hit the Papal standing section and to the left of the picture of the pope and his vices/virtues, there will be a 'request a crusade' button. Click on that, and it will give you a choice of heathen cities to smite (note: only non-catholic and excommunicated catholic factions are valid targets. You cannot crusade a non-excommunicated catholic faction, regardless of how bad their standing with the pope is).

To join a crusade (after starting your own, or after one has been started already), simply get a general/family member (has to be a general or family member, cannot be just a captain) + 7? (I think its 7 units, might be 6) and either right click on the general, or left click on the hire mercenaries button. At the bottom left of the scroll will be a 'join crusade' button. If you don't have enough units, or there is no general/family member present, the button will be greyed out.

Hope that helps.