1. The best way is never to let them get there in the 1st place. We started building Windows PCs in 1992 and every one built to date has had the OS on it's own partition.
2. Back in the mid 90s, some marketing dude decided that they could fool their customers and make them think their Hds were bigger than they were by switching from base 2 which all of computerdom is based upon, to base 10. Competitors squawked for a while but eventually they adopted the practice. SSDs held out with 128 GB and 256 GB models but everything now everything is base 10 w/ SSGs too. So now we have to twist our minds around the fact that a 1 TB HD only fits 1,000 MBs and no longer 1024. That's the reason why ya 250 GB SSD only fits 232 GB worth of files. For whatever reason 1 GB of memory on an SSD requires only 1,000 MB of file space and when used on a RAM stick it needs 1024 ... go figure.
3. I would highly recommend that you do a fresh install of the OS on the SSD with the HD disconnected. You can simply install the programs over themselves to keep the programs functional. And that leaves you in a positioin to boot from the HD if the SSD dies or OS there gets fudged.
4. Alternately, you can use a migration tool but that still leaves some flotsam and jetsam on the new OS install.
5. Another option is to install the OS to the SSD as described in 3 above ... and then look at the contents of each and delete from the HD whatever you see on the SSD.