Yes, the boots and lower part of the pants is a tricky area. The problem is, if the jute goes down to the boots, sometimes you will step on the jute, and can fall, trip, stumble, etc. Therefore, I had to cut the jute so that it did not get in the way. However, now my boots are not concealed. I had originally planned on not making a lower half to the ghillie, and the way I look at it, the pants covered in jute is a "bonus". While the boots could give me away, it is not very likely. If possible, I try to cover my lower half in the vegetation attached to the ground to offer more "natural" concealment. This typically helps solve the boot problem. But when making a quicker hide, such as relocating, especially to a position with limited veg, it serves a much larger problem.
As for what is best if the ground is mostly leaves and little vegetation, a tan based ghillie with some browns is nice. My ghillie is a all year round ghillie and has some spots of green. However, it blends in fairly well given the ghillie is predominately tan. It has been dirtied up, and is a faded tan, and looks much more natural, and offers good camoflauge. For any ghillie, I recommend a tan base. Great for when vegetation is scarce, and can also work when vegetation is abundant, as a lighter ghillie can easily be made darker with some vegetation added here and there.