Most servers utilize the IMAP protocol for accessing email. This actually replicates the data on the server with the data on the local machine and vice-versa As a result, anything done on your ipad will also replicate to the server which in turn will also replicate to eM Client.
There is another protocol, POP3, which does not replicate but instead just downloads all new emails to the client requesting the emails. Be careful, however, as it is not recommended that you mix devices with IMAP/POP3 which access the same mailbox, as this can cause problems.
Thanks for reply.
Whilst keeping the IMAP protocol is there any way I can keep emails on one machine but delete them from another one?
Not really if you are going to use IMAP. The whole idea behind IMAP is to synchronize.