It actually is helpful when putting data in separate tables to break it into separate transform maps. Especially if it is a simple matter of column A goes in table 1 and column B goes in table 2. It seems like a lot of work, but it is usually pretty straightforward and makes it easier to figure out what you were doing when you or someone else has to come back and update something in a year or whenever.
The exception is if your data requires a lot of scripting to make it go from the original data source to the target tables. If you are already manipulating and massaging the data, then it may be easier to combine that together and just script everything in the single transform map. You can create an onBefore script that will run for each row in the data source and then use GlideRecord queries to find and update all the information you need to change for that row of data.
