@Physicist (great choice, btw!):
If you don't need to sync your folders on a regular basis, - you don't need to "add" them. They will not show up in the list of folder in the Accounts View.
But you can access them in Aquamail by going to "other folders" in the Accounts View and in the disappearing "cabinet" menu. (There is an option to have "other folders" shown in the Accounts View, - I don't remember what's the default setting for that.)
Once you accessed a folder, - it will stay in the Accounts View for a set period of time (it can be tuned in the settings, by default it is 1 or 2 weeks, I don't remember).
And you can sync any of those folders manually at any point. So, if you do not need frequent access to those folders, I'd recommend not to configure them syncing regularly (that consumes memory and data).
However, at this point it is not possible to pin the folders in that list without having them synced. (Kostya is aware of the request to make that possible, - but it is not a crucial feature, so, I don't expect it to happen too soon.)
And, indeed, it is impossible to check-mark multiple folders and then choose to sync them all.
I am not sure, it might have been done on purpose, or just because there was no need for that: typically, with a mobile e-mail app, the modus operandi is somewhat different from that on a laptop/desktop, and you have more limited resources (memory, storage space).
For example, - I have tens of folders for some of my accounts. I "subscribe" to them in Thunderbird, but I don't sync them in Aquamail.
I hope this helps.