mutilple sets of for alignment

[Alaki]

I apologize in advance if my question is so trivial ...

Basically, for a given sample, I have a set of runs, some of them are paired reads some others are single reads.
I understand I can use the following for each types

MosaikBuild -q mate1.fastq -q2 mate2.fastq -st illumina -mfl 500 -out read.mkb

MosaikBuild -q mate1.fastq -st illumina -out read.mkb

Since eventually, I would like to use MosaikAligner to map these reads (from 1 sample) against a reference; I wonder, if I should merge these "read.mkb" files in advance or I should merge them after alignment ?

Thanks again