While syphoning, I simply keep the wand about 1-2 inches off the bottom to avoid the trub (yeast that has dropped to the bottom of the fermenter.) This helps keep the beer nice and clear. A lot of people I know like to transfer their beer to a secondary before kegging to help keep the unwanted trub out. I found if your careful, it's just an extra, unnecessary step, and extra steps always add the chance of either contamination or oxidization, both of which can cause off flavors in the final product.
After all the beer is in the keg, I add some CO2, than open the pressure relief valve to purge out any oxygen in the keg. I repeat this step about 3 times to ensure the oxygen is out. Than I move the kegs to it's proper location, and leave it hooked up to the CO2 for about a week. I'll pour a test beer in a week to see if it's fully carbonated, or if it needs more time. This is another one of those difficult sacrifices we homebrewers must make.