ok so when you place invisible platforms on top of a not perfecly flat piece of terrain the platform will have the height of the average height of the area it covers (or something like this, actually this doesn't matter) but if the ground is not flat, there where the platform ends any unit walking from normal ground onto the platform or vice versa will snap around strangely. Thats why you lower them into the ground. You first create the terrain only with the raise/lower tool. The platforms are only placed to apply their cliff level to the area they're placed. To Maintain any changes in the terrain you made with raise/lower (e.g. small hills that do not mean to be a new height level) you need to make the visible terrain the actual thing the units walk on, you have to lower the platforms into the ground so they do not actually walk on the platform but on the normal terrain. The thing is, that the platforms cliff level is still applied even if the normal terrain is above the platform. Hope this makes it a bit more clear