Assuming it is a frameless stencil, just a thin sheet the I do the following:
Find a nice flat surface and get together some spare boards of the same thickness as the board you want to paste.
Arrange the spare boards around all for sides of the board you want to paste so that there is a continuous flat surface.
Tape down the surrounding boards. Then align the stencil with your board and carefully tape it down at one end.
Now apply paste using a squeegee. If you don't have a proper one, a credit card will do. Try to apply the paste in one stroke. Some people say you can't do repeated strokes, but I find you can if you're careful. Probably need to do a few practice runs to get it just right.