The how really depends on the mod. Since pretty much every object and ability in Sins has its own entity file, the mods that just change existing values or add their own files generally aren't very difficult. For example, if you have a mod that makes pirate raids happen every hour instead of whatever it is now, that mod modifies the gameplay.constants entity only. You can easily combine it with any other mod that doesn't do anything with gameplay.constants - say if a mod made all ships have 2x everything (damage, hp, whatever). All you'd have to do is copy the pirate modified gameplay.constants over the ship mod's, and you just combined 2 mods.
In reality, few mods will be this simple. A lot of mods will end up modifying the same files, and often the same things in the same files. In such cases, assuming the mod release will be converted back to binary, there's nothing you can do. If one mod modifies Terran planets to have 2x the tactical, and another to have 2x the logistic points, and both are in binary, the modders themselves would need to merge the two. If they weren't in binary and you were handy with modding yourself, you could just add the additional modifications into one of the files.
Now, on top of that we have the Strings file. Anything new that gets added will often also have added strings in English.str to describe and name the new research/ships/abilities/etc. Since there's only one English.str, you'd need to manually pull out the strings unique to one mod, and put them in the English.str file of the other along with combining the GameInfo files..
As you can see, combining "simple" mods can be easy. Combining complex ones/total conversions won't be, and it will be up to the modders to try and make theirs as easy to combine as possible
Hope that helps!