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I use Top-Down method (Assembly Design). When I create a new Part I use faces, planes from other Parts in Assembly, and then Catia create External References in this new Part. This External References make impossible creation constraints
Okay, now I understand. You're designing parts "in context" with "contextual links."
Yes - you should be able to use the copied geometry in the External Reference set for assembly constraints.
But, if the part is "in context" the only constraint you should add is a FIX constaint in order to lock the part location & orientation to the same as the part your getting the external references from.
The "in context" part will have a green gear in the tree icon for that part instance.
If the icon shows a yellow gear, it does not contain external references (or linked) elements. This instance of a part can be repositioned/constrained in the assembly.
If the icon shows a brown gear, it is a secondary instance of the "in context" part and this instance can also be respositioned with assembly constraints.
Going back to your original post, external references are absolutely worth it! They provide associative links from the parent part to all the children parts. Making changes to the parent part will automatically be passed on to the children part through the linked geometry in the External References branch.
Yes - you will have problems if you try to change the external reference geometry in the children part, because those changes should be made in the parent part instead.
If you must change the copied geometry, then isolate it first to break the link and then make the change.
Try publishing the elements in your skeleton (top-down control part) before using them. Publish is more robust than than context. I have gotten some KIN to work with published links that would not work with context links.
Sorry, but I'm still confused by your terminology the Project 3D Elements is a Sketcher command, which is normally used within the Part Design workbench. When you say "Assembly Design", I'm not sure if you mean the Assembly Design workbench or you mean you're working in "the context of an assembly of parts."
I think you're asking if Project 3D Elements is a useful tool?
Absolutely, because it creates a link to whatever it is that you are projecting. So if the parent element changes, then the linked elements (the projections) change automatically.
Assuming you are creating the External References on purpose, these Links are very powerful things in CATIA, and they will really help you when you make to your designs by automatically propogating the change to all the effected features/parts/assemblies/drawings/ etc. But you must be more careful when you use Linked geometry - otherwise they can hurt you instead of helping.
If you don't know why you're getting the External References, and you're not sure what they are, then you could have lots of problems when you try to modify your design.
I'm not sure where you got your CATIA training, but this is one area where proper training is very important and can help you become a better and more productive CATIA user.