Put them in jars/containers as they are ready, or wait until everything is dry and do it in one hit, whichever makes more sense to you. There are no rules.
A small pair of wire "side cutters" makes cutting stems much easier than trying to use scissors.
Obviously, you will need to cut up pieces that are too long for your jars or buy bigger jars. How much have you been smoking today??
Also, believe it or not, not only is drying your flowers with their leaves left on better for final quality, it is also faster, due to the large surface area of the leaves. "Wet trimming" means all water must escape through the buds (and stems) and this can accelerate terpene decomposition. If the leaves are left on, most of the water will be drawn out by them, preserving a higher percentage of terpenes and cannabinoids within your flowers. Having the leaves on also protects the trichomes for falling off. Personally, I store my flowers with leaves left on and dry trim just before consumption. The leaves also protect the trichomes from falling off when taking buds out or putting buds into the jars. With the really small stuff, you can keep it for a rainy day or do as I do and give it to one of your friends, they will generally be happy to get some free flowers, even if they are small.
Hope this helps,.... Organoman.