The appearance of the pane(s) can be configured by editing
~/Library/Application Support/mr.pennyworth.AlfredExtraPane/config.json
Here's an example with four panes configured:
[{
"workflowUID" : "*",
"alignment" : {
"horizontal" : {"placement" : "right", "width" : 300, "minHeight" : 400}}
}, {
"workflowUID" : "*",
"alignment" : {
"horizontal" : {"placement" : "left", "width" : 300, "minHeight" : 400}}
}, {
"workflowUID" : "*",
"alignment" : {
"vertical" : {"placement" : "top", "height" : 100}}
}, {
"workflowUID" : "*",
"alignment" : {
"vertical" : {"placement" : "bottom", "height" : 200}}
}]