If you're letting Veritas manage the cleaning, then I don't think it matters what slot the cleaning tapes get put into ...
Just create the appropriate rule to catarogize the cleaning tapes when you inject them and you should be good to go ...

Of course, I could be wrong ...

The libraries will recognise media if the cleaning slots have been configured and will let you inject the media in to them but these slots are not visible to the netbackup application, therefore a when a 'clean now' operation is requested through the console it fails since the EMM database has no knowledge the media id's exists. The library in this instance will use the cleaning tapes as part of the autoclean feature only. I have read this may possibly lead to problems with inventory functions etc... if netbackup is not in control.

Right, so just let NetBackup put the cleaning tape into whatever slot it wants to.
Can you disable the cleaning stuff on the library itself? That might be necessary ...

This is what I am trying to do by deleting any cleaning slots that have been defined on the library. This in turn disables the autoclean feature. When an inventory is run on the library it just will not see this cleaning media in the mailbox slots...

http://seer.support.veritas.com/docs/275223.htm

I have used the above support article to create a rule for the cleaning media on the Dell PV136T libraries and this work perfectly. Since all tape libraires are visible to all master and media servers the one tape rule should apply to all. Just to rule out a problem with the barcode labels, I have used one of the cleaning tapes which has been successfully recognised in the other model of libary. Strange problem since there are 2 x Dell PV136T and 2 x ML6020, the rule works fine on the PV136T libraries but not the ML6020.

I use to encourage having the library do the autocleaning. The libraries would issue a cleaning request when it discovered read/write erros. I no longer support this type of setup because the library isn't smart enough to know if the read/write error is caused by I/O problems, bad media, or other external occurrences. The heads were getting blamed way too often and thus were being cleaned way too much. This causes the heads to become prematurely worn down. Now, I only manually clean the tape drives.