multinom

Hi Tessa,
To compare the fit of two models, you can first fit each one separately, and compare them using the anova() function. It will do a likelihood ratio test.
I think you have to construct your response differently, and not use "replica" to group observations.
The response variable has to be a matrix, with a row for each replica, and the counts on each patch in the columns. The explanatory variables will have as many entries as there are lines in the matrix. I now see that your covariates are patch-specific, which is more involved than what multinom() allows. Multinom() only allows an offset with that structure.
Maybe you will have to fit your data using a log-linear poisson model then, or function vglm() from the "VGAM" library can also handle multinomial data. Agresti, Categorical Data Analysis has a lot of info on the analysis of multinomial data.
Scripts for that book are available at http://www-stat.stanford.edu/~owen/courses/306a/Splusdiscrete2.pdf.
Cheers, Tom