On the menu bar, go to Tools > Global Options.
Click Navigation.
When adding items to the queue
Choose Transfer immediately to start transfer of the queued item as soon as it is dropped in the queue.
Choose Suspend to place the item in the queue, but to hold the transfer.
Choose Schedule to display the scheduling window when an item is placed in the queue.
When dragging an item to the local pane
Choose Transfer to current folder to send the dragged item to the folder currently listed in the Local Drives pane.
Choose Transfer to default folder to send the dragged item to the default transfer folder listed in General Settings.
Choose Add to queue & suspend to place the dragged item in the queue, but hold the transfer.
When double-clicking an item
Choose Transfer immediately to send the item to the displayed remote site or the default download folder.
Choose Add to queue & suspend to place the double-clicked item in the queue, but hold the transfer.
Choose Launch in viewer to open the item in the File Viewer program chosen in Helper Applications.
Choose Execute to run the item if it is a program.
Choose Edit to open the item in the File Editor program chosen in Helper Applications.
Remove successful transfer items from the queue automatically
Select this check box to erase items from the queue after they have transferred.
Clear this check box to keep items in the queue even after they have transferred.
Note As old items build up in the queue it can consume large amounts of memory. Selecting this option avoids the problem.
Auto-refresh the server (remote) pane after an upload
Select this check box to update the remote folder's listing after every upload to that folder.
Clear this check box to stop sending LIST requests to a remote site after every upload.
Switch from the Site Manager to the Local Drives Pane upon connection
Select this check box to automatically display the Local Drives pane when a connection is made.
Clear this check box to leave the Site Manager displayed when a connection is made.
Use NLST instead of LIST (retrieves an abbreviated listing)
Select this check box to retrieve a "simple" listing from remote folders that do not properly display their listing.
Warning: This may affect certain transfer options, and may list folders as files.
Clear this check box to display standard listings of remote folders.
Use absolute paths for delete, send and receive commands
Select this check box to send these commands properly for servers that do not support relative path conventions.
Clear this check box to send these commands for servers that support relative path conventions.
Use absolute paths for the LIST command
Select this check box to send the LIST command for servers that do not support relative path conventions.
Clear this check box to send the LIST command for servers that support relative path conventions.
Send the FEAT command upon login
Select this check box to ask the server for a list of extended features it supports.
Clear this check box stop sending the FEAT command, the server won't respond with a list of supported features.
Note: Not all servers support the FEAT command.
Use the logical parent (not physical parent) on CDUP command
Select this check box to return to the folder
you just linked from when clicking the Move up directory 
button.
Clear this check box to change to the actual folder the item resides in, and not a folder with a link to the item, when clicking the Move up directory button.
Enable PWD to determine current folder
Select this check box to see the absolute file path of a remote folder. This will show an item's true location on a server.
Clear this check box to send just a LIST command or a Change Working Directory Command when requesting a folder listing. This may not show an item's true location on a server.
Enable SIZE and MDTM to get remote file info before applying overwrite rules
Select this check box to allow CuteFTP Pro to check file size and modification time and automatically determine if it should replace an existing file with another file of the same name.
Clear this check box to see a prompt any time you try to transfer a file to a location that already has a file of the same name.