If you own a valid license of Visual MODFLOW Flex you still have access to Visual MODFLOW Classic. Many "old timer" modelers - including myself - continue using both interfaces depending on the actual project requirements and if required to get back to some of the older modeling projects. Nonetheless, migrating to Flex might be a bit strange as the user interface is quite different, but once you get accommodated it is much more flexible and efficient, especially with the last 3-4 major version releases. I'm not exactly sure what you are trying to do, but if the model is relatively simple, start by using the numerical modeling workflow which is conceptually identical to the Classic workflow. You have to create a starting grid, import or create surfaces by interpolating point objects in the Data tree, and assign them as layer elevations exactly as you would do it in Classic. You may then further refine your grid both horizontally and vertically as required.
There are a few tutorials coming with the Flex installation, and you may want to do the Airport tutorial that walks you along the steps of the numerical modeling workflow to build a relatively simple box model.