My first thoughts are that any software is better than none! How have they been managing so far if they are a large Company?
If you have different companies under a 'holding parent' - I believe it would still be better to have a separate accounting file for each as I don't know any software that can deal with varying VAT submissions.
Having said that - QuickBooks would deal with different companies all in one file by using the 'class' system - but this would need a strict implementation of every expense having to be 'classed' to the correct business - though how this would work for different VAT submission, I don't know!
QuickBooks will also deal with multiple VAT agencies - though this is more intended for businesses that may have, for example, partial exemption on certain goods - these transactions can be put to one VAT group, then when the overall VAT submission is made, it's easy to 'view' the adjustment that is needed via the second VAT group that's been set up.
QuickBooks Online is also about to release the facility to easily record CIS payments and deductions within its software any day now :-)