Faint red galaxies in the Sloan Digital Sky Survey show a puzzling clustering pattern in previous measurements. In the two-point correlation function (2PCF), they appear to be strongly clustered on small-scales, indicating a tendency to reside in massive haloes as satellite galaxies. However, their weak clustering on large scales suggests that they are more likely to be found in low mass haloes. The interpretation of the clustering pattern suffers from the large sample variance in the 2PCF measurements, given the small volume of the volume-limited sample of such faint galaxies. We introduce a method to improve the clustering measurements of faint galaxies by making a full use of a flux-limited sample to obtain volume-limited measurements with an increased effective volume. In the improved 2PCF measurements, the fractional uncertainties on large-scales drop by more than 40 per cent, and the strong contrast between small-scale and large-scale clustering amplitudes seen in previous work is no longer prominent. From halo occupation distribution modelling of the measurements, we find that a considerable fraction of faint red galaxies to be satellites in massive haloes, a senario supported by the strong covariance of small-scale 2PCF measurements and the relative spatial distribution of faint red galaxies and luminous galaxies. However, the satellite fraction is found to be degenerate with the slope of the distribution profile of satellites in inner haloes. We compare the modelling results with semi-analytic model predictions and discuss the implications.