After upgrade from 5.0 to 5.0.1 (Build 5028) Standard, I can no longer change publishing directory on folder right click in project tree (input box is disabled).

So FTP uploading to diffrent target folders is not possible.

Is there any solution?

it was always disabled. The main purpose of "Effective mapping" in the project folder properties is to show you the results of mapping (e.g. publishing directory relative to the account's root, URL and remote directory for the debugger).
In order to change destination for a subtree publishing, you neeed to add a new Mapping entry in the project properties.

In project properties dialog there is no mapping sheet, only Properties and Includes.

Top publishing directory is set.
Mapping Run Mode is System default

I am using 5.0.1 Standard edition.

Mapping settings are fully supported only in PRO version.

Thanks for your reply.
I must say that this is future is must-have for me and that is not listed in Versions comparison (http://www.nusphere.com/products/phped_verscomp.htm), so besides buying good php IDE editor I did not spent money well.

I'm sorry, that page is not accurate and missed this feature and I agree mapping for publishing should be enabled. Also, the page lists Intergration with PHP encoder as not supported by Standard version while actually it's supported (as of 5019 through 5031 builds).