You can send your maps as an email attachment from the desktop application (MindGenius Version 4 or later is required). To do that, switch to the Export tab and click 'As Email Attachment'. Send the email to an address that is accessible from your iPad.
When you view the email on the iPad you can tap the attachment and select "Open in MindGenius".
Alternatively, MindGenius for iPad integrates with Dropbox which is a free, personal online repository in which you can store files and access them anywhere.