Pulse Accumulator can register number of external pulses or do gated time counting.
Free running timer counter TCNT is your chronometer. Using input capture you capture timestamp (TCNT) of first pulse t1, then timestamp of second pulse t2. Frequency is 1/(t2-t1).
Regarding usage of input capture, I think you should read Section 10 of M68HC11 Reference manual. HC11 has similar input capture and output compare channels like in ECT
http://cache.freescale.com/files/microcontrollers/doc/ref_manual/M68HC11RM.pdf