Hi,
"Does that mean I have to model all the waste treatment processes in the input"
not really - if you check any ecoinvent waste treatment process, there this principle that I tried to describe is already applied. For your own processes, if a process is creating waste, and this waste goes to another process for treatment, the waste treatment process, then you should model it so that the waste treatment process delivers a service (treatment of 1kg waste) to the process where the waste is created, and in this process, the waste treatment service is input. You should change the sign to preserve the mass balance; the process producing waste thus has input of -1kg waste treatment service (for example), which is provided by the waste treatment process.
Hth,
Andreas