How is the amp powered?
Some smaller amps made specific to the bikes power off the radio feed and take that directly from an interconnect harness. That's a harness made to connect directly between the radio and the original large plugs that connect to it. You simply unplug the harness from the radio, plug the new short harness in between and plug that back in to the radio. Very simple and accounts for both power to the amp and outputs to the speakers.
Others are slightly more complicated; though still not overly difficult. A "switched" amp will have a (usually) large power lead that comes straight from the battery. A smaller power lead that is only hot when the switch or radio is on also goes to the amp and "switches" it on when either the ignition switch is turned on or the radio is turned on. A separate ground wire to the amplifier is also required.
An amp like this will also need to be fed the audio. The leads currently going to the speakers (with the exception of the 04-05 SEEGs for purposes of our conversation here) will now go to the amp. The HD radios do not but many radios have pre-amp outputs separate from their normal speaker outputs specifically for this purpose.
Whichever way audio is fed to the amp the output from the radio goes first to the amplifier. The amp will then have its own audio outputs. Those are what will now be connected to the speakers.
That's the very basics of it. Many variations on the theme with other accessory parts. But that should help get you started.