I'm not really familiar with these devices, but from what I read briefly, you've got some limitations. Assuming you use the divide function of the ecap module (divide the incoming signal by 62), you're going to have limited resolution. If the processor runs at 120MHz, and your input frequency is 85MHz, the best you can get is 120/(85/62)=85 samples/cycle. Or, said another way, worse than 1% error. If this is good enough, then you're all set.
Another way to measure frequency is to use the incoming signal to increment a counter. Enable the counter for a fixed amount of time, and let it accumulate lots of input pulses. Then divide the counter value by the enable time to get your frequency. For example, enable the counter for 100milliseconds. If you read out a value of 1,000,000, your input frequency is 10MHz. (1e6/0.1). This method will give you pretty accurate results.