When you make your isometric walls, be sure to create two separate objects, one that is a flat collision mask, and one that's the wall itself, because you will only want the collisions to occur on the base of the wall. While it is a planned feature to add custom collision masks, it hasn't been done yet so that technique is the next best thing
Also try out the 'for each ordered' condition. Add a family like blue or something to every object that is isometric, and then loop each blue ordered by its Y position, and bring it to the front. That will make the player go behind and in front of walls etc.