You indicate you know how to deal with inclusions (cut them out or position them where they are least seen (in the edges of the stone possibly under prongs) and zoning (place a color zone in the culet or across the full girdle of the stone). To determine what cut to use, look at the smallest dimension of the stone, which will probably be the depth. Since the next smallest dimension would be the width, you need to look for a width to depth of at least 60% for most stones. Higher RI stones can be a little less deep. If you run into thin rough, you can lower pavilion angles below the critical angle for the material if you use an apex crown, with no table and instead apex facets at about 8 to 12 degrees. The rest of the crown can be at low angles. In this way, you can facet a thin stone without a window down to about 55% depth. If you have more depth, you can chose a cut with a depth of 60% to 80% or even more, altho’ very deep stones will require a custom mounting. Once you have determined what to do about angles and design to accomodate the depth that you have, you can turn the stone face up and see what shape the outline suggests. You would like to follow the contours of the rough stone’s shape as much as possible. This could lead to a free form stone, or maybe your outline is close to a hexagon (with some crystal systems), a trilliant (like tourmaline down the C axis), a round, or some other shape like a kite or keystone. I am assuming that the stone is large enough to be a center stone of a ring or pendant and that you can design a piece or jewelry or sell an odd shaped stone because of its appearance and weight.
So, to sum up, you look at the dimensions of the rough and find how much depth you have and then work from there to a design with the appropriate depth (generally 60 to 80%). From the depth you turn the stone to look down into the center of it and determine a shape that uses as much of the rough as possible. If you have a very long, thin crystal, you may cut a long emeral cut or cut the stone in half to make matching stones for earrings, which gives you a slight premium over the price of the two single stones.
I hope this makes sense. I am assuming that you have access to a catalog of designs so that you can find shapes and depths for all of your rough. For special cases you might need a facet designer familiar with Gemcad to design something special. You can look for facet designs on the internet, particularly at facetdiagrams.org