Add additional instances of a source with the "add additional" option, not with the "add new" option.
Don't use the crop filter, instead hold down the ALT key and drag the source window handles in the preview to crop.
To apply different filters to the different instances, don't apply the filters directly (they will show up for all instances), instead create a group and put one instance into the group, then apply the filter to the group instead of the instance. This way the filter applies to that instance only.