If you want to add multiple directories at once use following code:
using (ZipArchive archive = new ZipArchive(@"c:\temp\myarchive.zip"))
{
archive.Add(
@"c:\temp\first.dir\*",
"/first",
ArchiveTraversalMode.Recursive,
ArchiveActionOnExistingFile.OverwriteAll);
archive.Add(
@"c:\temp\second.dir\*",
"/second",
ArchiveTraversalMode.Recursive,
ArchiveActionOnExistingFile.OverwriteAll);
}