I don't think you can have a ot of input, but certainly I might be able to say something like 'I'd like to have a cover that could be the same basic design for all the books in the series so that they're instantly recognisable, not only as a series when all together, but also so any fan who bought the first one would recognise the second one as soon as they spotted it.'

Other than that, not really, I don't think, though they may listen to you if you hate it, I suppose.