How to save a file with smart object?

I have just created a file from LR2, by choosing 'open as smart object' in PS.
I then added a cloning layer and did my cloning.
When I wanted to save the file, instead of PS turning it in into a PSD with the same name, I now suddenly got the 'save as' pop up screen and '-2' as the recommended name. The original folder where the file came from was not shown.
I don't know what that's all about, but I'd prefer it would just save the file as a PSD and automatically show the file alongside the NEF in LR2, like it does when I don't use the 'open as smart object' feature. Is this typical for working with smart objects opened straight from LR2?
Any help will be greatly appreciated.
Marsel

Well, like this you open the file s a smart object, so if you want to now clone on a layer but want it to be a part of the smart object then you go to the layer panel and click on the smart object's icon there to edit the smart object and you hit save (command S) and it will save with that layer to your original.
then when you click the tab or the window that has the original opened as smart object those changes will be reflected, but you will not see your cloned layer active as that is a part of the smart object and you have to open the smart object to get to it.
What you say! Yes that is what I say that is what a smart object is, you are using the smart object as a part of another document( that is why you are being asked to save as, as this new documents you can now make changes which will not effect the original which is the smart object unless you rasterize it which will make it no longer a smart object.
What good is a smart object, well there are many say you are using this document or image if you wish in say five projects and the image has been retouched and it is determined it should have some more work done to it all you have to do is retouch the smart object and all five projects are updated.
You see smart.
And of course you can d things to all five projects that can be different from one another on other layers without ever destroying the work you have done to the smart object.

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