I don't understand exactly what you mean by combining the workbook. It would be very helpful to have some screenshots, the twbx files, or a more thorough description of what you would like to achieve. However I do have some thoughts based on what you have shared above:
If you are using different custom SQL in each workbook, these are different data sources according to Tableau, even though they are based on the same database.
If you want to use one published data source for the two workbooks, I would recommend publishing one data source that is set up so it works for both, and then creating calculations/filters in the separate workbooks for the information you need to be different.
If you mean you want to actually copy all the sheets into a single workbook, but half the sheets will use one data source (one custom sql query) and half another, this is also fine. The two separate sql queries will be treated as two separate data sources. You will need to choose whether you want to publish the data sources separately from the workbook or not, and how often they will refresh. https://onlinehelp.tableau.com/current/pro/desktop/en-us/help.html#publish_overview.html has more information on publishing workbooks and data sources.
Hope this helps!
You can import one into another and can still refresh