If you’re finding that Photoshop CS6 or CC is flattening your layers, there’s a really simple fix. If you know the option exists, of course–it doesn’t exactly leap out at you.
When you go to convert your color profile from, say, Adobe RGB to sRGB (Save your file first, then Edit > Convert to Profile), the very bottom option option is “Flatten Image to Preserve Appearance.” Uncheck that to stop the layers from flattening.
You’ll then get another popup, this one asking whether you want to rasterize the smart objects. This really depends on how complicated your smart objects are, but for simple smart objects the “Don’t Rasterize” option tends to work well.