I had some problems with the emulator button in eclipse, too.
Some times it just wont't fire the emulator up. I actually have no guess why this is (maybe it opens up in another dimension where you can't see it :P).
I worket around this issue by simply not using the button ;).
I start the emulator manually.
On linux after creating your emulator configurations you can start an emulator from the command line.
In your Android SDK folder there is a subfolder "tools".
You can run the "emulator" program and give it the name of the AVD configuration as first argument.
emulator @My_AVD_Configuration_Name
You have to put the @ token in front of the name.
Then you can install your APK file by using the "adb" program.
The "adb" program is in the "platform-tools" subfolder in your Android SDK.
Just write.
adb install -r MyAndroidApp.apk
I hope this helps a bit :)