If the screen really says "Secondary Master", you should have no problems. The way labels work for IDE ports is: there MAY be one or two IDE ports, and they will be called the Primary and Secondary IDE ports, so it appears your machine either has another IDE port you are not seeing OR it is using the "Primary IDE Port" label for something else like a set of SATA port(s).
Now, for EACH real IDE port, you can have up to two devices on the port sharing it and the ribbon data cable. THIS is where the designation of Master and Slave becomes important. EACH IDE port MUST have a Master to work, and MAY have a Slave in addition. So you have set the jumpers on your HDD to Master and it is recognizing that. Your confusion is solely in the fact that it says that HDD is connected to the Secondary port. Don't worry about that.
What HDD will be our boot drive? Is there a boot drive already installed somewhere, and you are installing a second HDD for data? What you write suggests that is not the case. It looks like you want to have this new HDD become the only drive, and hence the boot device. If so, in BIOS you will need to find the place where you specify the Boot Priority Sequence. Most people would set that to try the optical drive first, and then the HDD second, and no other devices. Just make sure the new HDD you are installing is designated here as a boot device, whether the second one or the first. It does NOT have to be the Primary Port Master to serve this function.