You might want to look at some wider boards. Usually you can find 1x10 and 1x12 boards which have very few knots in them. The number of knots is not as important as the location of those knots. If they are all on one side of the board you can rip a few clear pieces out of the other side, and then find another project where you can use the remainder of these boards.

If you are still stuck with pieces which have large knots in awkward places, cut out the knots with two long, parallel, diagonal cuts -- one on each side of the knot -- and then glue the pieces back together, but without the knot. You'll simply have a scarf joint where the knot used to be. While the cuts are long, you'll only be shortening the board by a bit over the actual size of the knot, so a 10 foot board with a 4 inch knot is going to "shrink" to about 9'8"

You'll probably be scarfing shorter boards together to get the length you need, so, assuming you use good glue, adding an extra scarf here or there is not going to significantly affect the strength of these parts.

Hope this helps

PGJ