Intensity mapping—the large-scale mapping of selected spectral lines without resolving individual sources—is quickly emerging as an efficient way to conduct large cosmological surveys. Multiple surveys covering a variety of lines (such as the hydrogen 21 cm hyperfine line, carbon-monoxide rotational lines, and [C ii] fine-structure lines, among others) are either observing or will soon be online, promising a panchromatic view of our Universe over a broad redshift range. With multiple lines potentially covering the same volume, cross-correlations have become an attractive prospect, both for probing the underlying astrophysics and for mitigating observational systematics. For example, cross-correlating 21 cm and [C ii] intensity maps during reionization could reveal the characteristic scale of ionized bubbles around the first galaxies, while simultaneously providing a convenient way to reduce independent foreground contaminants between the two surveys. However, many of the desirable properties of cross-correlations in principle emerge only under ideal conditions, such as infinite ensemble averages. In this paper, we construct an end-to-end pipeline for analyzing intensity mapping cross-correlations, enabling instrumental effects, foreground residuals, and analysis choices to be propagated through Monte Carlo simulations to a set of rigorous error properties, including error covariances, window functions, and full probability distributions for power-spectrum estimates. We use this framework to critically examine the applicability of simplifying assumptions such as the independence and Gaussianity of power-spectrum errors. As worked examples, we forecast the sensitivity of near-term and futuristic 21 cm × [C ii] cross-correlation measurements, providing recommendations for survey design.