Format-Table is going to cause you problems there. It only returns strings, so Sort-Object isn't going to find what you're looking for. Using Select-Object is a better choice (you can pipe through format-table at the end to get the table output):
Get-MailboxDatabase |`
Get-Mailbox |`
Select-Object DisplayName,IssueWarningQuota,ProhibitSendQuota,`
@{label="TotalItemSize";expression={(get-mailboxstatistics $_).TotalItemSize.Value.ToMB()}},`
@{label="StorageLimitStatus";expression={(Get-MailboxStatistics $_).StorageLimitStatus}} |`
Sort-Object -Property StorageLimitStatus,TotalItemSize | Format-Table
As to the sorting, just list the properties you want to sort by, as in the example above.