If the spinnaker halyard/retrieval sheet is set up correctly, there doesn’t have to be any change in the amount of that line that is on the deck with the spinnaker either up or down, and it shouldn't come far enough back on the tramp as to become fouled with the mainsheet/traveller sheet line when sheeting the main sheet off the rear beam.
You haven't simply, got the spinnaker halyard/retrieval sheet line too long (or longer than is necessary) have you??