At least on my Xubuntu machine, any attempt to start the graphical client fails with the message: "Cannot obtain a lock on data directory /home/rena/.bitcoin.  Bitcoin is probably already running." So, any time you want to use the graphical interface you need to first shut down bitcoind, losing all your connections. Or you can leave the GUI open all the time (sitting in taskbar since the option to minimize to tray is disabled), which is kinda inconvenient and makes the daemon not really a daemon anymore.

Can the GUI app not simply work as a frontend to bitcoind, letting it run at all times?