CS6 can definitely open the CS5 saved native Illustrator ( .ai ) files. In order to properly open the files saved from Illustrator CS6 in CS5, you will need to save the file to CS5 version.
Illustrator provides you with the option to save a file which is compatible with its earlier versions.
This can be done by selecting Version as "Illustrator CS5" in Illustrator Options dialog which appears when saving .ai file, shown as below:
This saved file can be opened in Illustrator CS5 without any issues.
This is great, thank you.
Another question though is...
I have opened this file in CS5 and it doesn't contain a font that I used in the CS6 version. If I accept the substitute, do my work and then save, when I come to open it up in CS6 again, will the font be back to what it was or will it still be the CS5 substitute?
It's things like that which I'm worried may be a complete hassle.
Font will be the substituted one. This is because you saved the file with different font. But you can definitely replace the substituted font when you open the file back in CS6.
Please have a look at the instructions provided on the help page: http://help.adobe.com/en_US/illustrator/cs/using/WSCA212715-FEFA-4cbc-BFC9-FE28E2FCC110a.h tml
Look for the instructions under the section "Find and replace fonts".