i have been an exclusive Wacom user for many many years now, i actually think using a mouse is kinda awkward now :-D
my setup is doubleclick on the lower side button and right on upper, and for apps that require middle mousebutton i set it up as middle on the lower. That works very nicely for me.
I have the wacom to the right of the keyboard, but know many wacom users prefer to have the wacom infront of the keyboard. I like to have it to the side so i can easily access the full keyboard for shortcuts that are very important to be efficient in AE.
As you have found out there is some mousewheel behaviors that is not as easy to perform with a wacom. There is the scroll wheel on the Wacom tablet that you can use, but that require you move your keyboard hand quite a bit, so its not so fast and i tend not to use that very often, and just don't use some of the mousewheel features that are in some apps.
Im looking for a new keyboard and are thinking og gettting the new Logitech Craft when/if it comes in a 105key nordic edition, that has a builtin multipurpose wheel at the topleft that could be helpful for at least us right-hand users.
If you use Chrome as your browser of choice, i highly recommend to download the addon called "scollbar anywhere" that makes it easy to scroll most websites by flicking the pen anywhere with eg the right button held down.
Then you will find out some applications are just not tested with wacom users before being released, where they require a very precise click where the pointer cant move any pixels before registering the click. Some Adobe apps have had this in the past, Premiere being bad at one point, AE for one version many years ago too, but they are mostly fine now.
Any plugin that uses a custom UI can have problems, eg Video Copilot Element is a bit frustrating to get into numerical value input mode, and a particular bad example has been Colorista that has such bad precision controls of the color wheels when using a Wacom.
Keep using the Wacom exclusively for a couple of weeks and you will soon surrender your mouse to the graveyard, overall its a much more natural and pleasant to work with a pen :-D
Robert