One way to help get your ink up nearer the head is that you can disconnect the ink line above the head and using a syringe, you can pull ink from the cartridge up to that point. This helps a little with getting ink up that far. Or you can even disconnect the damper and pull ink to the damper.
If you're lines to the waste tank are clogged, then you will definitely have a problem with getting suction on the capping station. As others pointed out, keep this cleaned so that it does create a good seal. We had to change one of these, and we actually ordered a whole maintenance station because at that time we were not aware that you could order just the capping station part of it. It is a lot cheaper but a littler harder to replace because of the short lines and spring underneath, but it is not too difficult.
If those lines are clogged though, you may have to disconnect those little lines anyway to flush them out. There is a little plastic adapter that goes from those small black lines to the clear lines of the pump. We ended up using a syringe with cleaning fluid to push out the clogs in all these lines when our started junking up. It can be time consuming and tedious, but keeping if you can get it cleaned out it can save you a lot of time. And something we learned too with our printer being down for quite some time is that if you are going to be down for awhile, put some cleaning solution down through the capping station to help clean it out so it doesn't clog up. We were doing that every so often to clean out any ink that was going into it when we weren't even able to do cleanings through the printhead because of problems.