I did my PPL at WLAC and there are a whole raft of options available payment wise as shown on the website.
You can pay as you go, buy a number of hours (5 or 10 hour anytime are on the list) or as you say pay the lot up front.
It sounds as if there has been some misunderstanding. What you won't be able to do is pay in parts and get the same discount & benefits as if you paid in one lump. If you buy the whole package you get the discount rate AND the exams included. Not saying that's a reason why you have to go that way
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I've paid them in pretty much all the different ways on the list with no arguments or problems... go in and speak to Ops rather than wait for a reply to a letter. It does sound like the problem you are having is that you are trying to arrange a bespoke finance agreement... "give me the price and benefits of paying in full upfront and I'll pay you in installments." It's worth asking but you can't be too offended if they say no!
Best of luck wherever you choose!