When reinstalling the OS just select the partition that does not have windows on it. Easies way to do this is to have a bootable OS on a flash or hdd.
How to create a bootable http://www.macworld.com/article/2367748/how-to-make-a-bootable-os-x-10-10-yosemi te-install-drive.html
Once the bootable it made switch off the mac then plug the flash or hdd in. Press the ( alt or option key ) and power on. This will ask you from where you want to boot off. Go through the setup until it asks you where you want to install your Yosemite to. Select the partition that does not have windows installed on it.
Wait for the installation to finish and thats that.
If you do not erase the OS partition you will do an over the top installation and this will keep your current data on the device, if you want the clean install, erase the partition first and then run through the step above.
Good luck 🙂
D