Based on the information I would suggest you do it this way.
1. Create a Control-M Tables called "Initial" and "Incremental" and create individual jobs for each type of 'batch'. Lets say create 5 jobs for 5 batches in Initial Table called A1, A2, A3, A4, A5 and create a File Transfer Job FTF_Initial which should take conditions from all jobs A1 to A5 (condition names should be unique with 'AND' logic between them, meaning until all conditions have been added FTF job should not start).
2. Similarly, another 5 jobs for 5 Incremental jobs, B1, B2, B3, B4, B5 and another FTF job called FTF_Incremental all in "Incremental" table. Here also, the FTF_Incremental should take conditions from B1 to B5 in a similar fashion.
3. Now based on your needs schedule the Initial and Incremental Table. Whenever the batches/jobs will run it will ensure that until all required jobs have run the File won't be sent to third application.
Advice: It is also advisable to choose Application and Group name distinctively for easier identification in GUI.