Well you kind of did things a bit wrong.
When you installed OS X on the new SSD and went through Setup, there was a opportunity there to transfer your account, apps etc., from the old HD using a SATA to USB adapter (or enclosure)
Also after the fact is Migration Assistant in the Applications/Utilities folder but then you have two accounts on the SSD and duplicate files in each account (have to reduce obviously). Later you can delete the original account on the machine, but I always like having two, even a small one, just in case I can't log into the first one.
You also could have used Carbon Copy Cloner, since it's the same OS X and everything, just switching hardware.
CCC gives finer control, so you can exclude a lot of large files etc., so you can fit everything on the smaller SSD.
So Setup Assistant, Migration Assistant and CCC all would have transferred Apps, I think CCC would be the best as it's a cloning tool, it images everything and the others may exclude things.
Of course you need to enable TRIM on the SSD or it will wear out soon
How you want to go about things now it up to you as only you know what you've got and where.
I would just start all over from the begining.
As you should know, you should be able to hold option/alt on a wired or built in keyboard and boot from the external HD with a SATA to USB adapter or enclosure (some are not bootable) and use Disk Utiltiy there to format the internal SSD and then use CCC from there.
This is what most people do when transfering everything (in OS X, not bootcamp) to a new drive, just in your case you have to make sure to fit under the SSD limit.
"ds store" is always very exhaustive in his answers. I can only say some apps can be transferred to the external disk with no problem although some related libraries (and especially 'preferences' file) may still need to be on the main HD. This are normally the apps you download and drag&drop into the Apps folder. Apps thah need an installer shoulod be removed and reinstalled onto the external disk.
PLEASE NOTE: be sure to have a backup of your entire 500HD before performing any change in the system.