I used this method for a 20x10 board where I had a stencil, but no jig to fit it it all into for alignment:
To find out if you like it or not it's good enough.
An old credit card works as a make-shift scraper if you don't have one.
Better is something of the same material that the stencil is.. stainless steel sheet in cc size as the edge is sharper and gives better results.
Just remember to scrape under a 45 deg angle to the pads, to get them filled easily without air-gaps.
Might need several passes and there is no problem to do several, just don't lift the stencil in between and make sure the surface you do this on is flat and stable to not have anything move. The tape you see in the picture hold everything pretty stable and keeps alignment of the stencil to the board well enough for 10 or so boards.
Paste I used the one that you can find all over ebay/aliexpress. Not the best, but does the job for prototypes.
Smallest pitch was 0.5 on this and worked pretty well.
PS: I didn't use kapton stencils yet, nor do I intend to, seem a bit flimsy.. YMMV though.