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A trifold needs to have the fold-in panel slightly smaller in width than the other 2 panels. The paper thickness determines the appropriate panel size, but for general purposes, 1/16 inch smaller for the fold-in should suffix.
For referencing the pages of a trifold, use this numbering scheme: front 5-6-1 and back 2-3-4.
You can lay this out with two 11 x 8.5 pages OR 6 single pages arranged in a group of 1-2-3 and 4-5-6. Using the 6 single page method requires a version of Indesign that allows modifying page sizes. NOTE: you can set up 3 equal size panels, but this can create a folding issue.
To achieve the 1/16 inch smaller panel, create guides/pages with the following widths: [front 3.625 - 3.6875 - 3.6875] and [back 3.6875 - 3.6875 - 3.625]