What I tend to do with fleets is include the whole lot of ships I intend to use, if I have some ships I want to order seperately inside the fleet I'd either just use the alt-click feature to select all units of that type or select what I want to and assign it to a control group (ctrl 1-9)

I have noticed that when you are making frigates and/or cruisers the shows them in groups of 10 in the empire tree when you have the stack option turned on. You can also shift+click on these stacks of ships to create fleets when you have multiple fleets you want to create in the same gravity well.

For example, if you had 30 Cobalts, 20 Garda's, 2 Kol's, and 10 Kodiak's all in the same gravity well, and you wanted to make 2 fleets. Let's say 1 fleet with the 2 Kol's and 20 cobalts and then everything else in another fleet. You could shift+click on the two Kol's and two "10-groups" of Cobalts and assign them to group 1. Then all you have to do is click on the other group of Cobalts, the 2 groups of Garda's, and the group of Kodiak's and assign them to group 2.

I haven't tried this as I was producing the groups, I waited until they hit the 10 cap before assigning them, so not sure if it will work the same in that situation.