I think you have this the wrong way: you have uploaded the *.csr file and got back the *.cer
Now, with the *.cer file received from Symbian Signed and with the *.key file you have from the Publisher ID conversion, you are ready to sign applications and install them on device. Whenever you see a reference to Developer Certificate (or DevCert) that's where you use the downloaded *.cer and the *.key file. Whenever you are told to use the Publisher ID, use the converted *.cer and the *.key file.
To sign a sis file, you use Carbide.c++, Qt Creator or signsis.exe
signsis.exe unsigned.sis signed.sis cert.cer cert.key