48 measures would typically have 4 measures in a system (across). But you can often solve the problem with more measures in a system (check out the 96 template option). A barline can be added either left or right of any space the cursor is in. The player will understand the barline placements and staying within the 12 systems (at least currently) is recommended because that is the limit we have designed and tested for.
Have a look at Brazil (in the Jazz 1300) as an example.