Some operate on a retainer - At the start of the contract all activities and timescales are agreed and an overall fee is agreed sometimes paid in stages and sometime all up front (stages is usual I believe)
Others operate on a commission basis IE they approach the various trade shows and media outlets that their clients wish to gain exposure through and push them for "Agency" rates which are usually around 10-15% off the gross rates. They then charge the clients the original Gross rate and are invoiced by the show or media company for the net (less the discount) rate and keep the difference hence they are paid only each time the clients agree to their strategy and allow bookings to be made.
As per their package they will charge. Every firm has their own package and the difference in price, but the difference is not much, as they charge they will provide exact services.
Every agency works differently and charges differently. You won't find a fixed set of guidelines of how they charge.
Agencies operate differently depending upon workload, client and activity. Also suggest you need to match your cost model to any pricing model for it to be effective.
I can understand that it will charge for each activity it carries out but surely a marketing agency also provides help with strategy, segmentation, etc. Do they charge on a day rate for this? And should I be expecting a retainer to be offered to which can cover the strategic side of this?