Simple answer: AS YOU INSTALL a program, DON"T CLICK CLICK CLICK CLICK through it, slow down and READ IT. You will always see a OPTION or CUSTOMIZE which will let you select things like, what path (where to install) you want the program to install to (i.e. default is C:\program files(x86)\Steam\Common\nameofgame). You just change it to what you want it to be on the 'non default' drive.
Now I do need to address what you said, and I believe your doing it backwards, and would cause more problems then solve with how your design is. Please take a moment to understand, a SSD is limited space and when you get over 75% of filling it up it starts to 'slow down' and not perform like a SSD normally does. The fastest way to fill up a SSD is with games, especially as only LOAD SCREENS benefit from SSD, SSD do NOT improve the game FPS or load faster, etc. It is just the way ALL games are designed are not taking advantage of SSD that way (YET!).
So normally the OS goes on SSD, with all main apps (Skype etc.) but when you get to other stuff (Steam, Games, etc.) you install those (as I noted above) to the LARGER HDD. What I mean by larger is HDD is 1TB+ SSD is usually 256GB and under. If your brave enough to buy a 512GB+ SSD = goes nuts man! and install a couple games (no waiting during loadscreens) for your pleasure on the SSD
Hope this helps.