Yeah the water down there is pointless if there's no smoke going through it. Compare it to a normal bong dude.
Dude... Really?... Well, just take the "second chamber" off. Just suck out of the pen (im assuming it's a pen) and use it as a bubbler. Then it will actually hit.
Tape, glue, sealant, silicone, melted plastic... Check this out. http://forum.grasscity.com/artists-corner/288221-simple-double-chamber-bong-diagram.html
Make a hole so the downstem goes through the water. Use the hole on the side as a carb. How can you own a slide and not know how to make a bong?
... A crayon? My guess would be its not hitting because smoke can't travel through a crayon, but maybe that's just me. Edit - Or my second guess is I read marker as crayon, and the marker is actually a hollow tube, which at that point I'd go back to the "actually sticking it in the vagImeanwater* point brought up earlier. And if it is indeed an actual marker, not hollowed, read my original point with marker substituted for crayon.