Managing your Android applications is very simple. Click your Android device from 'Devices' and you can then see task 'Manage applications' if you have right mode activated from your Android you can start browsing your device apps. (See How to connect my Android?)
To uninstall application from your device click 'uninstall' -button from browse view and you get confirmation dialog where you still have a chance to cancel.
To install new applications to your device select Applications under 'Online resources' and there you can find all places which offers applications, select GetJar.com. When you want to install application to your device select application and click 'Install selected to..' -button and you get list of devices where you can install that application. (Note: Android phones will only show up when right connection mode is active.) Currently you can install one application at the time, but it wouldn't be a problem to install multiple applications at the same time or even use drag&drop to installtion, this would only be a UI change.
After you have selected the target device you get final confirmation dialog and you can still cancel installation.