Follow e100's advice. Here's why: you have (or your client has) a budget, and the difference between the cost of a standard job and a custom job is substantial.
The cut lines in a template are called die lines. They are your guides to where the cuts will be made. Your folder will be made from card stock which will be cut after it's printed using a cutting die, then folded and glued.
Any commercial printer that does this kind of work has existing dies which he uses over and over again, so the cost of making them can be recovered a small bit at a time (amortized) across many jobs.
If you invent your own shapes, or use someone else's template with die lines that don't match what your printer already has, he must get a custom die made just for your job and he is going to pass on the full cost to you, perhaps with an added markup. Unless you have a very good reason and can afford the extra cost, then, it is better to pick your printer and use their template.
Always, always, always consult your printer any time you're doing something you haven't tackled before. The printer wants to do a good job. His reputation depends on it, after all. He will be happy that you asked, and happy to give you the help you need to get the best product for your client. Happy clients bring you more work, and tell their friends. That's the surest way to grow your business.