I just took a quick look at our mojoPortal database, I think you'll just need to insert rows into mp_forumsubscriptions (one row for each forum ID/user ID combo). What I would personally do is query this table after subscribing myself to a forum or two, just to be sure about the data format. Then you can set up insert statements that draw from a select join of mp_users and mp_forums. Some users might already have subscription rows out there, so you might want to clear all existing subscriptions before starting.
SQL tool will vary according to your platform. We use MySQL and I like HeidiSQL for that. If it's SQL Server you can probably use SQL Server Management Studio or something equivalent. You could also use the delivered SQL Query Tool, although I haven't used that one myself.
As always, double check your work, and most importantly, be sure you have a good backup of your database before you start!
Jamie