Subdomains or subdirectories


I’m trying to setup a new network and need some advice on which structure to use -subdomains or subdirectories.

The network i am building will be similar to say schools in a state. So for example i have a list of 3000 schools that i will want to add onto my nework with basic contacts details etc and a few plugins like articles and videos that i have preselected for them. Users that pay to to activate their account will then be able to make changes to these articles and videos etc.

I would prefer to use sub domains as the ministies name will appear first but i am worried that setting up as subdomains will mean a huge amount of work.

Can you please advise which method i should use?