I haven't actually tried super soaker CTF, but this is how I would play it:

Each team has its own base with a flag displayed. No restrictions on amount of guns or power, but the teams should be rougly even. One can store extra guns in a base instead of carrying them, but they can always be stolen.

The object of the game is to obtain the enemy's flag (from their base), return it to your base, and touch it to your own flag in it's default position. If this is done, announce your team has made a capture.

The water guns are used in a "one hit kills" manner. If you are hit by any water, you must drop any flag you are carrying, hold your gun over your head, and return to your team's base before continuing playing.

Team members are allowed to bring a friendly flag back to its base after soaking an opponent who began to capture the flag.

The team that makes the capture wins. Of course, you could play first to 3 or 5 captures, or something similar.