Which Hydraflow program are you using? Hydrographs and Express will allow you to enter up to six drainage areas with independent runoff coefficents and will calculate a composite runoff value. Storm Sewers will allow you to enter up to three drainage areas per node with independent runoff coefficents. Click on the runoff box (C or CN) and it will bring up a dialog box that will allow you to enter multiple drainage areas and runoff coefficents.
You are correct that the Hydrographs and Express extensions will only allow for three of each type of TR-55 Tc (sheet, shallow concentrated and channel), however, the Storm Sewers extension will allow you to specify an independent Tc for each inlet and then design the system by considering both the inlet time and the pipe travel time. Although less convenient, note that you can enter a user Tc value so should you need to utilize more than three shallow concentrated flow paths for example, you could calculate by hand and enter the value manually.
Be careful when using more than a couple shallow concentrated flow patterns. In my experience, the flow tends to transition to channelized flow before I have used all three shallow concentrated flow pattern options. Also note that you can use this TR-55 interface to enter pipe travel time, simply put in pipe cross sectional area and wetted perimeter of your pipe and it will calculate Tc as a function of full flow (gravity) pipe capacity.
Jason Slocum