Can I use the in silico digest with a draft assembly?

Yes. The only thing you have to make sure is that each contig is in a separate fastq file. An example to do this is:

mkdir split_genome; cd split_genome; awk 'BEGIN{filename="file1"}{if($1 ~ />/){filename=$1; sub(/>/,"",filename); print $1;} print $0 >filename.fa;}' ../genome.fa; ls -1 `pwd`/* > ../scaffold_list.txt; cd ..;

But you have to notice that you will miss those fragments/locations that start and ends in different contigs.