I've been using SD cards more and more just as you mention and I think you'll be ticked with the benefits of having double the storage.
Here are the tools I use to get the data I need on relative speeds so I can choose what should be stored on the drive and what shouldn't go there.
The Daisy Disk tool is really stellar for quickly seeing which chunks of data are big enough to be worth your time to handle. In my case, the first chunks I will move to the card are:
- 20 GB of logic files from
/Library/Application\ Support/Logic to the card
- 40 GB of Photos Library if the automatic compression algorithms don't shrink the files on my local storage enough for my tastes.
- Less seldom used Virtual Box and VMWare virtual machine storage drive files
I also use BlackMagic disk tester to check how the speed of both drives is actually so that I can keep the things I don't care about being slow on the slower SD card (or pay more for a faster SD card).
OS X would run fine with your entire user folder on the SD card, but make sure you have a second admin account on the boot volume if you go that drastic route.
As far as opening files - most applications will run just fine if you use Finder aliases or command line sym links to point to the storage card once you move files off the boot volume.
Also, if you are bugged by HiddenStorage in your setting, download the full version of DaisyDisk - it runs for free if you have bought the app on the MAS and adds two critical features for me: scanning as an administrator and collecting files to then delete them
Be sure your Time Machine backup is backing up both the boot volume and the SD card before you delete things, but I've had no issues running OS X like this from 10.7 Lion through the betas of 10.11 El Capitan.
Some apps are cranky, so I would leave all system files where they are and worry about things that are 10 GB or more in size rather than trying to micro manage dozens of small relations that don't yield significant storage savings on the boot drive.
In your case, you can use iTunes to locate the iTunes storage on the external SD card and moving the iPhotos Library is trivial as well. Move it from Finder and then open the new file. Delete the original file once you're sure things work and/or you have a solid back up.