Should a special issue follow the regular frequency of the journal or separately?
Both ways are possible, but usually they are called differently. If the issue is replacing a regular issue, it is called special issue.

If the issue is added to the standard set of issues, making an extra one, it is usually called supplement. And even here the conventions differ; some supplements are published with a regular issue, and some are published separately. Most often, they are numbered as 1S, 1A or alike, but form an integral part of the volume.