the best is to use our Feedback Forum (http://boxcryptor.uservoice.com/forums/100207-general) for suggestions, so that all users can vote on these.
1) By default, BoxCryptor automatically checks for updates on each startup (this can be deactivated in the Advanced Menu), but not every version is rolled out via the automatic update (e.g. the current 1.0.9 is not, but 1.1 will be).
2) This is already suggested and it is on our todo-list. You can vote on this feature here: http://boxcryptor.uservoice.com/forums/100207-general/suggestions/1772537-support-multiple-encrypted-folders?ref=title