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I'm assuming the pool is a rectangle other than the swimout, and you mean a flexible pool cover that you roll up or fold up - the type that looks a bit like bubble wrap? There's a few choices of how to handle the swimout. It's important to know that the vast majority of heat retention is from reducing evaporation. The cover is a great way to keep a pool warmer to extend the swimming season and reduce costs.
A. You can leave the swimout uncovered, because it's a relatively small % of evaporation protection that you lose.
B. Or you can fold in that section before rolling up the cover, and then the rest of the cover (and reel if you're planning one), need only be as wide as the main body of the pool.
Go to the 5:20 mark of this video to see what I mean:
Install a Daisy Solar Cover and Roller - YouTube
C. Or you can use a reel wide enough to include the wider section, and roll up the cover from the wide end or nearest the swimout if it's not right at the end.
For all covers, you can buy a standard size and trim to fit. For both of B and C, you buy a cover wide enough to cover the swimout, or for some suppliers, provide a detailed layout and see what their price is. It may not be much more.