I just edited my battleship so that it can load cruise missiles. I saved it as civ3x.bix because I thought those modifications would load next time I start the game and be the default ones used... and then I can procede with loading a custom map, or loading one of my saves... but it didnt.
How would I make this modification the default one used?

I don't know much about that aspect, but you can just load your modification as a scenario, and then make a custom map.

Did you start a new game? If you did that should have worked. The rules are included in the save so no saved games will be affected by your change.

I would recommend you not do that though. There are a few bugs that seem related to changing the master scenario. In addition, if you screw it up there is no way back short of reloading PTW. For a final reason every patch has over-written this file so your hard work will be lost when Firaxis releases the next version (it'll be soon).

Make a scenario instead.

warpstorm, I dont understand.

Any changes made in the editor will not take effect until you start a brand new game (or scenario). Any previous saves will be played under the rules that were in effect when they were started.

and as warpstorm said, and I suggested as well, just make it a scenario.