The existing external antenna is already amplified from the base, I'm not sure you can actually 'amplify' the antenna, the amplification is of the signal that is received by the antenna, think of the base as a turbo, just pushing what its already being fed through at a stronger rate. A different dB gain in an antenna will make a difference, but the dB does not equal power, so a high dB antenna is not high power. You need to have the correct dB antenna for the situation you are using it for, for example, open plains a 9dB antenna will have a stronger signal further, but will will not be as effective in hilly country, whereas a 3dB antenna is good for reception in hilly areas, but has a more limited distance range. There are 'multi load' antennas that cover both bases, but I have no dea what types of antennas are actually available for the VE.
I am having radio reception issues with my car which is currently being investigated by Holden, they have replaced the radio module, replaced the amplified base and antenna, all to no avail. I have seen a vid taken on a phone of the diagnostics program running where the signal strength can be seen fluctuating up and down all over the place as they are driving, this was after the radio module was replaced which showed them that it was not the problem.
As for your question about what effect the amped antenna will have on an already amped base, well unless you have additional wires to power it, it will only draw its power through the already amplified base, so it can't hurt anything, but I would be very interested to hear what your results are.
I will try to find out how to access the diagnostics program which was being displayed on the iQ screen and post back as it may help others who are having the same trouble.