Some shops will allow you to top up with your own money over the £1000 limit although they are not supposed to. Most of the big shops won't allow this though. Keep it in mind as well that if you do find a shop that will allow you to top up over the £1000 that the bike won't be insured for the full amount, the bike will only be insured for the £1000. So in the event of a damaged/stolen bike, you'll take the hit. I know this as the shop i work for allowed this to happen last year. The bike was stolen. Customer only insured for £1000 and he had to pay a £250 excess, so he lost out pretty badly.
Some companies can get the limit upped to more than £1000 but they need to apply for a credit licence agreement to do this. This costs the employer so most are not willing to do it.
Hope this helps some.