I may not be understanding what you are trying to do but if you are trying to have, say, a blue flag for "Geocache|Unknown," you would go to that pushpin set and select Properties and go to Symbol and click on the down-arrow to pull up the available pushpins and select the blue flag symbol. You only have to do this once for all the pushpins in the set which, following this operation, will all be marked on the map with a blue flag. If you want a green dot for "Geocache|Traditional," repeat for that pushpin set and select the appropriate symbol from the drop-down, and so forth. In other words, you can change the symbol for all the pins in any given set with just one simple operation; you do not have to do it for each single pushpin in the set.
If there are pushpins in a set that you do not want in that set, you can pull those you select out of the set by going into the list of matching pushpins and selecting them (ctrl-click) and the right-click and "cut." Now, go to the map and paste them (all together, not singly) onto the map and a new pushpin set will have been created which is populated with only those pushpins you have pulled out. You can now rename that set and/or choose a new symbol, if you like.