I don't see any reason why the stock radio and dash mounted speakers would stop working if you installed an aftermarket deck in the glove box etc.. unless you disconnected the original one.
Here is the tube installed in my '65
In my truck the tank is more centered towards the drivers side which allows enough room for this to fit.
Here is a view of the cab
And another
Other than the deck in the dash most people wouldn't even know it had a stereo let alone amps, changer and sub.
Here is the speakers
I have the amps mounted under the seat on the drivers side and the changer is under the passenger side.
I am far from, and never profess to be an expert on audio but I feel that a clean install with quality wiring is more beneficial than huge amounts of power and crappy installation.
On our trucks getting rid of the "tinny" sound from all the metal interior is paramount. I am planning many updates to the interior as I go through the restoration process and while the basic system will stay in place I am going to change the mounting in the doors and replace some wiring (this system was installed in 1998) and the speakers.
I found that it was much less hassle to install the system when I had the seat out and installing the carpet kit.