EmbroideryStudio provides a dedicated Hooping Mode toolbar which allows you to specify multiple hoopings for large designs, both manually or automatically. In order to align consecutive hoopings during stitchout, you can include registration marks for each hooping via the Multi-Hooping tab of the Options dialog.
It is important to minimize color changes in a design. If you activate color optimization in the Multi-Hooping tab, this is automatically applied to the design when generating automatic hoopings.