My second question is, most of the jack stands have a flat or low curved head to put the car upon them, but the cars have protruding edges around them with the height of 1 inch or more. Won't this cause a damage if I try to put the stands below them?
You can get slotted rubber adapters that you put on top of the jack-stand, the look something like this:
They aren't generally expensive and then allow you to fit the jack-stand under the chassis frame rail in the same way as the factory scissor jack does.
This is how the service manual suggests doing it.
If you're using rigid stands and a trolley jack for the actual lifting then the jacking point(s) are like so:
You're probably wonder how you do this if you're using the scissor jack to lift - and the answer really is that you don't. Jacking/support points are where they are for good reasons.
There's probably a suitable point to place the stands as-is somewhere on the subframe (which obviously would allow you to lift from the jacking point using the scissor) - but I don't know Highlanders well enough to know where that would be and, well, this is not a good area for experimentation.
Lifting and supporting 1800kg+ of car to do work on it is something that when it goes wrong you consider yourself lucky if that outcome is just expensive and not life-threatening!