Do all endtables/tables/counters/couches, etc have to be the same height in order for the objects that people put on them to be positioned corectly? Like if you make an end table too short and you put an object on it, and it floats in the air, is there a way to fix that?

As far as I know, I had a problem with a wall shelf I made. This tutorial by Numenor was very helpful. http://www.modthesims2.com/showthread.php?t=82685
It will show you how to get your objects placed on the the different serface heights
such as low tables and counters. My problem was placed objects would hang through the bottom of the shelf. I fixed it by lowering the shelf with Milkshape3D.

You can adjust the height of the slot in the CRES. In the "Content" tab, select the slot from the "Blocklist" drop down menu. (The slot will most likely be labeled something like slot_table_std_0.) That will bring up the "cTransformNode" tab. Under "Translation", you'll find values for X, Y, and Z. Z is the height. Standard height for end tables is 0.8. Enter your new value (if you don't know it, go back to your 3D editor. I just build a box around my object and see what value I get for Z.) Once you've done that, commit, fix integrity (Tools/ObjectTools/Fix Integrity), save and go try it out in your game.

Good luck!

Cool, thanks! And if I do that it only adjusts the height for that one object, correct?

Correct.