Database Migration

Thank you BilltheCat and InsiteFX for your feedback, your comments are much appreciated.
My development is an application that allows companies to track progress of their own jobs, quotes and ultimately the profitability of their jobs, rather than a traditional website, blog or shopping site. The app runs on a subscription basis with companies opting in and out on an ad-hoc basis. I maintain a single (separate) database for all users (company, contact, login details) and a seperate database of prefixed tables for each companies data. This approach is very scalable as I can add/remove sets of prefixed tables as customers subscribe/unsubscribe, and can create new databases/connections as the number of customers increase. Regarding analytics, I have little need to perform analytics on the customer data, as in effect this is their property, and the data means little to me except total number of customers (from user database) and total number of jobs/quotes processed which is run periodically run using a pretty simple foreach query using the connection and prefix stored which is stored with each customer record.
My questions was really centered on the use of Migrations: whether I am using them correctly, i.e. 1 routine to create new tables, and another to update existing tables, and secondly should I/how do I use the force method to reuse the create routine. Any help with this will be much appreciated as I cannot fathom how to do this? 
Also, if you have any knowledge on this is there any additional documentation as I do not understand Up and Down, whether both should be specified and what they are used for?
Any help is very much appreciated.

Again thanks.