You may consider to use QB Desktop 2021 with the one time license to manage 3 separate company files. Then you will use a MTD Excel Bridging app. They provide a HMRC Approved web based solution for submitting your VAT returns for MTD. You can use your own excel spreadsheet or use an export Excel or CSV from any accounting program. It's free for the first year and GBP 30/year/organization for the second year onwards. They are also offering special price plans for accountants.