It doesn't matter where the custom function is placed. Once you execute the INTRDEF, the moment the interrupt edge occurs, after an interrupt latency (< 2ms) the interrupt service custom function will be called and in it it you must start the timer using:
TIMERPV[n] = xxxx ' n is the timer #, xxx is the timing value.
When the timer times out its contact will be turned ON and the ladder logic takes over and the timer contact will handled like regular contact in the ladder logic portion.