yes it is perfectly ok to base your shooter and loader on seperate bases.
heck its what i do as i lack extra infantry and plenty of heavy weapons.
i have just 2 regular guardsmen on their own bases and a heavy weapon on its base. before a game i will paint a stripe on the gunner and loaders base. this way i can keep track of whos where.
now theres this special rule that says if your opponent has as maining wounding hits as their are members in your squad they can force you to roll a wounding for one member. if they hit the gunner the weapon is now useless. if they hit the loader the weapon keeps going (at least thats how i understand it)
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