When the delay period of the Zak-OTFS carrier is greater than the delay spread of the channel, and the Doppler period of the carrier is greater than the Doppler spread of the channel, the effective channel filter taps can simply be read off from the response to a single pilot carrier waveform. The input-output (I/O) relation can then be reconstructed for a sampled system that operates under finite duration and bandwidth constraints. We introduce a framework for pilot design in the delay-Doppler (DD) domain which makes it possible to support users with very different delay-Doppler characteristics when it is not possible to choose a single delay and Doppler period to support all users. The method is to interleave single pilots in the DD domain, and to choose the pilot spacing so that the I/O relation can be reconstructed by solving a small linear system of equations.