Hi jah,
Your device only has 1 timer with two channels.
It doesn't have a TBM.
So there is only one counter to rollover, so 1 overflow bit/interrupt.
You will use 1 channel as your IRQ, in the interrupt handler read TPM1CxSC (x depends on channel you use) then clear bit 7 of it. Now you can do what you wanted.
This will still allow you to use the timer and the other channel for other purposes as you have not interfered with the timer at all.
Think of input capture as a very fast bundy clock (the clock used to check when emploees of a factory start/stop work in case this word is not universal).
You clock on at 11am (11am recorded on card)
Clock "rolls over" once at midday
Clock "rolls over" a second time at midnight.
You clock off at 2am (then resign because hours are too long) (2am recorded on card)
So you have worked for 1 period - 12hours
plus 1 hour before and 2 hours after = 15hours
This is exactly how the timer works and how you have to interpret the results.
You can configure the spare channel to clock on/off accurately or just read the timer for rougher timing.
You can use an interrupt to count the rollovers or just poll the overflow bit.
If you just want the pseudo IRQ ignore rollovers.
Hope this helps
Regards David