Better workflow in Atmel Studio 6 for building and transferring program
Wow, you're certainly rebuilding your project the hard way. 



There is a single click (or keystroke) solution to rebuilding any changed files, and programming the mcu with the new binary. You're looking for the "run" command, which is F5 in a default install. You can also access it from the debug menu, you want the "continue" command (no, I don't know why it's named that). 



You can also hit the green "play arrow" (in the blue box) on The toolbar to rebuild and launch with the debugger attached. It's the shortcut to the run command. The Non-filled "play" arrow (in the red box) will rebuild and launch your project without the debugger attached.

Re: Tooltips - The Green arrow's tooltip is Start Debugging. It should probably really be
Start *with* debugger. The Green arrow outline's tooltip is Start without debugging, which is more clear.
I suspect a lot of this is behaviour inherited from Visual Studio, which Atmel Studio is built on. If you're familiar with one, the other becomes a lot more predictable.