  We present improved methodology for including covariance matrices in the
error budget of Baryon Oscillation Spectroscopic Survey (BOSS) galaxy
clustering measurements, revisiting Data Release 9 (DR9) analyses, and
describing a method that is used in DR10/11 analyses presented in companion
papers. The precise analysis method adopted is becoming increasingly important,
due to the precision that BOSS can now reach: even using as many as 600 mock
catalogues to estimate covariance of 2-point clustering measurements can still
lead to an increase in the errors of ~20%, depending on how the cosmological
parameters of interest are measured. In this paper we extend previous work on
this contribution to the error budget, deriving formulae for errors measured by
integrating over the likelihood, and to the distribution of recovered best-fit
parameters fitting the simulations also used to estimate the covariance matrix.
Both are situations that previous analyses of BOSS have considered. We apply
the formulae derived to Baryon Acoustic Oscillation (BAO) and Redshift-Space
Distortion (RSD) measurements from BOSS in our companion papers. To further aid
these analyses, we consider the optimum number of bins to use for 2-point
measurements using the monopole power spectrum or correlation function for BAO,
and the monopole and quadrupole moments of the correlation function for
anisotropic-BAO and RSD measurements.
