Will a 69 rearend work in a 68 camaro? Or what is the different?

Yes...

The only difference may be the spring mount, if it is a 'mono' and you try to put it in a 'multi' car it will be to shallow for the spring and cover plate to fit correctly - and visa-versa, if it's a 'multi' and you have 'mono'...

But axle width and spring mount pad spacing is the same for all 67~69 Camaros.

The inner brake line clips on the axle tubes are in a different location on a 69 ( slightly higher), but a little tweaking will make the lines fit them.
Also there is a difference in the yokes regarding u joint retention. there are also 2 different width yokes regarding U joint cross dimensions, same as 68.