Frost heaves and drainage are closely related. Basically, you need to get rid of anything that doesn't compact (topsoil) and replace it with material that compacts into a porous but very solid mass. For a patio or walk, the standard is at least 6" of base (gravel, crushed stone) plus a couple inches of sand. If you are placing interlocking pavers, you can compact the sand, lay the pavers and recompact. If you are laying irregular bluestone or other flagging, you need to leave some uncompacted sand to level the stones.

Roots are bad news. They will heave any pavement if allowed to remain, even if they start deeper than the base. They are the reason many good contractors will go down at least a foot with compacted base, as it will eliminate all but the deepest, and they might not show up for years. Don't leave any rocks in the base - they will telegraph through to the top.

I am working on a stone retaining wall apx. 18-20 inches tall with various rock types. the base is shallow and i think adequate for the height but only now have roots concerned me. the wall is at the sidewalk in front of the house with room for the roots to grow under the walk. Do i
cut the tree roots off and risk tree damage? what to do???

Also, mortar for the odd sized and shaped rocks is a problem to apply. Any tools info. and or suggestions would be greatly appreciated.