It depends on the type of quilt I'm designing.
I designed a landscape quilt and for that one the method was "wing it". I had a general idea in my head, hung a piece of muslin, and started by glueing bits of fabric to it and it evolved.
I designed a baby quilt and a chemo quilt in a similar fashion ... laid down the "foundation" quilt (in each case they were simple pieced quilts that did not require a "pattern") then drew out the applique I planned on using and attached to the foundation quilt.
For quilts that are going to be pieced together and require *math* ... I prefer to use EQ7 to design it which insures that the math at least is correct. After that, I may use EQ 7 to print foundation patterns for PP, or I may use MS Word to print foundation pieces.