I love to use onagers both defensively and offensively, and I try to have 2 or 3 in each of my "full" stacked armies.Typically I play H/H and they are great for lowering the moral of the enemy troops. I usually use a combination of rocks and fireballs - rocks for the general because it seems to me that they are more accurate and fire for the infantry.
Onagers dominate bridge crossings and are very effective in forts. When I decide an enemy city must fall there is no waiting to build siege equipment - just move in, knock down the walls, destroy any troops near the breaches and march right in.
Guineawolf is correct about the wall types in defensive fighting - onagers cannot shoot over the larger wall types but in that case I just put them in the town center and wait the enemy to enter - I can usually get off several rounds before they close and most times the enemy reaches your town center piecemeal which allows me to cut them to pieces before they even can close for combat.
I have to admit that they do require some micro management to get the most out of them and so they don't mow your own men down along with the enemy. Because I use them regularly they "rank" up quite quickly. With 2 or three onagers with triple silver chevrons there is no enemy that can stand my bombardments for long. As far as moving them around on the strategic map - make a plan, anticipate where you need to go, get them moving early and you will find that it is easy to have them where you need them most. As a side note I use allot of spies to keep tabs on my neighbors armies. With a decent intelligence network I never have a problem fielding the "wrong" kind of army.