There's several ways to fill a carto. I think I've tried them all and prefer dripping into the top of the carto. The following is what I do:
A tip that I use when pre-filling the carto is to plug the center air hole with a wooden tooth pick. This blocks any unwanted e-juice from getting into the tube that can cause flooding.
I hold the carto at a slight angle, and rotate it around as I drip liquid onto the polyfill. When the fibers look like a slushy drink, I shake the carto down like a thermometer. This produces the same effect as a centrifuge, forcing the juice down into the carto.
I return to adding more drops, and shake it down again. Repeat this process until the polyfill will absorb no more liquid.
The carto is now ready to vape. No need to blow out the carto, as no liquid got in it. No need to let the carto sit, it's already as set as it can get.
If this is for a cartotank, the rest of my method is explained here:
http://www.e-cigarette-forum.com/forum/blogs/baditude/3710-carto-tank-setup.html