Many different ways to do it. My preferred approach is to source a stencil from Pololu. That makes it super easy to get the right amount of paste where I want it. Simply select a 4-mil thick stencil for normal work, and 3-mil for a fine job (i.e. where you have microprocessors that have pins with a 0.5mm pitch, for example).
Simply surround the board with other spare boards, tape down, then position the stencil carefully, tape as well. spread the solder paste with a thin stainless steel applicator blade or putty knife. Place all components, run through you favorite reflow technique - I happen to use a re-purposed toaster oven with the rocket scream reflow controller.
The components come out clean, the solder is usually perfect and requires no additional work. This is especially important for chips with finely-pitched pins as those are very easy to bend during subsequent cleaning-related touch ups. I use no lead, no clean Kester NXG1 solder paste
that I bought (I think) at Techni Tool.