After submitting ticket 1776325 to support I was asked to submit a feature request. As it stands ftp quotas are not restricted to the total quota for the account that is creating them. It is very confusing for our customers to have a quota of 200mb set to their account and subsequently be able to set the quota for an FTP account to 1000mb without any warning or error that they have exceeded the account quota. If I were to give a suggestion, the creation of ftp accounts should check if the addition of the quota will exceed the total of any ftp/mail account quotas combined, as to set a reserved amount of space on the system that is still below the total account quota. There should also be a quota reservation for the pubic_html files that is set by default for an account during creation so that ftp/mail account quotas do not fill the entire account quota. An example for an account with a 200mb quota:

50mb reservation for public_html
150mb for ftp/mail account quotas

There is probably a better way to do this, but something should be done to constrain and identify quota usage.