Here's what you can do with that Yosemite installer.
Do not run the installer - yet.
Make a copy of your installer.app somewhere else, so if you have difficulties, you don't need to download the installer again.
Make a bootable drive (separate partition on an external drive, or create a dedicated installer on a flash drive, which is what I have.)
Boot to that installer drive or partition, and then you can decide.
I would do it in your situation by:
Backing up your SL drive.
Boot to the Yose installer, run Disk Utility, and erase the internal hard drive.
Install Yosemite, which will now be clean.
On first restart, the system will ask if you want to migrate from another drive, so do the migration from your external backup that you just completed.
This process may take the longest time, and you'll have everything from your old system, updated to Yosemite, along with the possibility that a few apps will be reported as not-compatible with Yosemite. Take care of those few, if you need to do those replacements for older software, and you are back up and running.
Or, you CAN choose to just upgrade your SL drive. Be safe, and back up your SL drive before you begin.
Apple does have a page that tells you how to make a bootable drive from the installer
http://support.apple.com/en-us/HT201372
Here's another site with the same goal:
http://osxdaily.com/2014/10/16/make-os-x-yosemite-boot-install-drive/
Both require some familiarity with the terminal.
But, I use the DiskMakerX app, which makes the process easy.
http://diskmakerx.com