I usually prick the top with a pin and when I've done for the day, I wipe the top off with a damp rag to get any excess glue off before putting the top on.
The glue does get thicker in time. Mine got thicker faster when I was leaving it on my sewing table that has a lot of direct sun contact. I leave it in a dark chest now, making sure it stands up right. It hasn't gotten nearly as thick. You can put some acetone in it to thin if it you need to. I've tried that once or twice. It does work, but I have been too afraid to put too much acetone in at once, so I probably don't use enough.