I do it this way. What's not absorbed can be sucked back into the bottle by squeezing it to create a vacuum and then using it to suck up the excess from the top of the carto. You quickly learn how much to put into the carto cap. I put the carto into the end cap and leave it for 15 to 20 minutes. Slush on the top will soak in and generally nothing is left in the cap. It's a good way to get good saturation of the filler.
After the initial fill, I drip in a few drops as needed until the top of the filler starts to look a little slushy.
There are basically three methods that I use, depending on the cartomizer.
1) Syringe and needle, I use 18g sharp needle. Especially effective with Boge cartos, as those tend to be very tightly woven and are generally a PITA to fill properly the first time. The needle puts your juice exactly where it needs to go and the syringe lets you measure the amount of juice accurately. The drawbacks? It's work and not everyone owns a syringe.
Other options: an oiler bottle
or dripper caps:
Dripper Caps
2) Condom method, as shown in Phil's video. Works well with Boge cartos, but I find it messy--lots of wiping afterwards.
3) Dripping!!!! The best and easiest for your cartos (and other non-Boge cartos wit loose filler). Just tilt and slowly turn your cartomizer as you drip down the walls into the filler, just like pouring beer.

Don't worry too much about the center tube; a little juice in there will prime the coil--just blow out the excess.