Preferences for the Multi Clipboard are set on the Preferences page under Window > Preferences using the Node 'Multi Clipboard'. The preferences page looks as follows:

You can configure the following behaviour:
By default, the Multi Clipboard is empty when Eclipse is started and all contents are discarded when the workbench is closed. If you want to keep the contents of the clipboard between sessions, tick the box 'Persist...' and provide a writable directory in the entry 'Directory'.
If persistence is enabled, the contents of the clipboard will be saved in a file named 'multiClipboardContents.xml' in the configured directory when the workbench is closed. They will be reloaded when the workbench is opened. Saving and loading happens irrespective of whether the Multi Clipboard view is activated.
By default, the contents of the clipboard can not be changed from the content-details dialog. If you want to enable editing contents through this dialog, tick the box 'Allow editing contents...'. See 'Viewing/Editing the Multi-Clipboard contents' for details on how the dialog works.
By default, the number of potential entries in the Multi Clipboard is not limited. However, especially when you persist the contents when the session ends, it may be useful to limit the number so you do not need to manually clean up old entries. This can be done by ticking the box 'Limit...' and giving a value in the field 'Limit to:'.
If the Multi Clipboard is configured to limit the number of entries, it discards the bottom entry when it is filled beyond this limit.
In case the Multi Clipboard holds more entries than the configured number when you change the configuration, the new limit takes effect only after restarting the Workbench.
In addition to the number of entries of the buffer, you can configure whether new entries should be added at the top of the list (pushing the existing entries down) od should be appended. Adding entries at the top of the list is the default behaviour. Note: In case you configure the clipboard to add new entries at the end of the list, when a maximum number of entries is configured aht that number is reached, no new contents will be added to the clipboard.
By default, the actions 'copy to Multi Clipboard' and 'Cut to Multi Clipboard' leave the standard clipboard untouched. However, you can change this behaviour by ticking the box 'Also copy/cut to standard clipboard'.
This is especially useful in case you want to use the keyboard-shortcuts 'Ctrl+C' for copy and 'Ctrl+X' for cut to also fill the (first position of the) Multi Clipboard. In this case, what you should do is to tick the 'Also copy/cut to standard clipboard'-box, which forces the actions you usually perform using the standard Multi Clipboard shortcuts 'Alt+C' and 'Alt+X' to also fill the standard clipboard.
Once they do this, you can safely use the key-bindings page (Workbench > Keys on the preferences dialog) to re-assign the shortcut 'Ctrl+C' to the action 'Copy to Multi-Clipboard' in the context of editing text and do the same thing with 'Ctrl+X' for the action 'Cut to Multi-Clipboard'. Below is a screenshot of the key-bindings page after the assignement for 'Copy to Multi-Clipboard' was added.