We check in online in advance every time.
When we use online check in, we have already paid in full so I can't answer your question about paying your final package charges. Otherwise, there's no additional charge for using online check in, etc.
The advantages are that you are then in their system, and they have your room preference requests. Then, when you arrive at your resort, your entire package is ready to go -- your KTTW cards, everything -- they have everything ready to hand to you (you just need to show a credit card and drivers license). They have separate lines for people who checked in online, and if there is any line at all it moves very quickly. I would estimate it saves a minimum of 20 minutes when it is your turn with the CM (using standard check in). Also, those standard check in lines move a LOT slower, since it takes so long to manually check each guest in.
We've gotten exactly what we've requested (when you do the online process, they ask you to put in order a set of room preference requests).
Online check in is generally not recommended for people who have very complicated room requirements, nor for people who may not like the room they are assigned by the system in advance of arrival (although again, our family has never had an issue with this).
When we checked in at the BC in June, a CM standing outside the front doors anticipated our arrival (our town car driver had to give our names at the security gate), greeted us by name, checked us in on her iPad, and walked us to the desk where we were handed our package and room keys. Took about 3 minutes.