You won't condition in a secondary. Secondary fermentation, clearing, lagering all happen in an non-pressurized environment.
Conditioning is the process of allowing natural fermentation processes to carbonate a beer, usually through the additions of sugars prior to putting the beer in a closed environment (keg/bottle).
If you want to condition you have to either keg/bottle before fermentation is complete (a rather exact science) or you have to add sugars for the yeast to consume so that it can create the CO2 that you require. Assuming you add table sugar, this will increase your ABV and dryness of the beer, but it is a very small amount on normal beers. I am not sure if conditioning to 3 volumes (certain Belgian styles) will affect the taste of the beer.
One other difference is that you can call a conditioned ale a "Real Ale", but not a forced carbonated beer.