The following is an excerpt from page 18 of the Warhammer Annual 2002 release with an expanded explanation by Gav Thorpe regarding how to accurate distribute hits from templates, in particular war machines.

This is probably a good place for a timely reminder. Generally (although some vary), weapons with templates automatically hit models wholly covered and affect partially covered models on a D6 roll of 4+. This rule is an absolute - if a tiny bit of the base is under the template or outside the template this is a 4+ roll, none of this messing about trying to judge if a base is half under or more, or similar shenanigans. If in doubt, it's more likely to be a partial hit than a full-on hit and hence roll a dice for it (see diagrams 3 and 4).