I want to use Zend Encoder from PhpEd editor. Is it possible to encode whole project from phped? I though it is possible but how can I do this?

As far as I see you'd run zendenc.exe with appropriate arguments in order to have files encoded. From the IDE you'd open Tools->Settings->Customization, add new Menu, have it "execite with Shell", put command line containing zendenc.exe and its arguments. Besides arguments you may want to add macros like @FName@, filter by *.php;*.inc, and enable "show this command in Workspace popup".
If source file directory or file name may contain space(s), you'd enclose corresponding macros into double quotes, like this:
"C:\Program Files\Zend\bin\zendenc.exe" "@FName@" "@FName@.encoded"