Categories and tags can be a very useful tool to help make a blog/website more navigable for users and boost SEO to boot. However the specific execution of these features are very much a matter of personal taste and discussion of the subject quickly leads to confusion. This is even more the case for a blogging platform such as Jekyll, which has both few plugins to automate the process and best practices. I myself am guilty of blindly using the very straightforward YAML declarations that Jekyll supports without any real forethought. Wordpress however provides very explicit documentation on the subject, which we can use as a good starting place.
Very simply, categories describe the gross structure of your blog, tags label specific entries. By analogy consider a publication, categories would be the table of contents, tags would be index headings. With this in mind we can anticipate that there will always be at least as many tags than categories, most likely more. The exact number depending on the breadth and depth of topics you choose to blog about, and the level of specificity each category contains. Generally speaking, tags describe something about a particular post, categories group several posts together. Once you have come to a decision how you will use categories and tags in your blog, consistency is key to make the most of your conventions. Another point to bear in mind, more specific to tags, is to make sure to use them effectively. Tags can be both underused and overused, ideally - I use the term very loosely here - you want each tag to be used more than just a few times, without being used for any and every post. Another way to think about this is whether or not the tags actually inform or help users. Analytics services could be helpful here to indicate user flow through your blog.
In practice, the first step is to think ahead: anticipate the breadth and depth you could possibly write about. Although this might not be entirely realistic, it will help prevent the problem of tagitis in the future. Beyond this, you may wish to think about how a user may navigate using categories or tags. As mentioned above, Jekyll tends to have a fairly sparse set of plugins, though there are some authors who have looked at this specific issue.
All the best,
Tom