I’m not familiar with the problem you describe, so I need to understand more precisely what you’re talking about.
What “tools” do you mean, exactly? What happens when you try to run a tool from the wrong directory? What do you mean by “tools directory”? What files do you copy into the “tools directory” to make it work?
Aren’t these command-line tools in the “bin” directory? In any case, they should be added to the path automatically by the Panda3D installer. So I’m a little surprised when you say it doesn’t work.
Of course, it certainly won’t work if you use the “./” prefix to your command; you should type “dae2egg model.dae model.egg” instead of “./dae2egg model.dae model.egg”. The “./” prefix means “look only in this directory for this command; do not search the PATH.”
Could this be your only confusion? Or does it not even work if you omit that prefix?