The biggest effect on running, as opposed to start up, speed (with regards to disks) will be where your applications store the data that they read and write. A sensibly-written application should keep its data (including preferences) in a separate place from the application itself (typically somewhere in your home folder,
/Library) so moving the Applications folder shouldn't affect this.
While loading a data file may be slower from a hard disk than an SSD, most applications don't read and write large amounts during their run except when you explicitly open or close files, though there are significant exceptions, such as video editing software. You might, however, want to look at scratch disks that large applications (Photoshop, for instance) use.
All this reading and writing will slowly degrade the SSD, though. To be honest, you seem to be using an SSD the opposite way most people use it - most people keep the OS and applications on it for fast start up and minimal read/write, and keep data on a hard drive which can better withstand large amounts of reading and writing.
If you want to improve the speed applications actually run at, your best bet is to add more memory. Applications should (mostly) load themselves into memory at start up, but some of that may well get paged out into virtual memory. When that portion gets paged back in, there's a delay. If you have enough memory to avoid it being paged out in the first place, you avoid that delay.