I'm looking for an explanation on the freebayes parameters --pooled-continuous/--pooled-discrete, but can't find it anywhere.
What do they do, and when should I use them?
Did you read freebayes -h? It shows some information, though admittedly leave a lot of room for interpretation:
Assume that samples result from pooled sequencing.
Model pooled samples using discrete genotypes across pools.
When using this flag, set --ploidy to the number of
alleles in each sample or use the --cnv-map to define
Output all alleles which pass input filters, regardles of
genotyping outcome or model.
However, there is plenty of further discussions / sources of information around, which should get you going: