Mek, are you asking about getting a full super off the hive or frames out of the super? Prising supers apart that the bees have really sealed up can be a problem. A friend of mine always chamfers the top corners of his boxes to leave a nice gap to get a hive tool into so that you can apply some pressure to part the boxes. That saves a bit of hive tool damage to the edges of the boxes too.
If your bees are the sort that uses lots of propolis to glue the frames in, it's a good idea to use your hive tool to lever the frame that you want to take out sideways to try and separate it from its neighbor then it's just a case of using the hook on your hive tool to lever each end of the frame up - sometimes a little bit at each end until you get it up/loose enough. Even then you will still occasionally get a top bar that will break rather than come out peacefully. Hoffman style frames where the end bars only touch for about half the depth of the frames helps a lot in these cases because the bees don't have as much surface to stick together and you don't need as much force to separate the frames.
The bees will certainly build in the lid if they get short of space and some bees will do it even when they have heaps of space. I'm not sure what type of lids you are using, but I'm assuming you have migratory lids with vents in the side. A lino/vinyl mat on top of the frames in the top super (under the lid, leaving a bee space around the edges) helps with burr comb in the lid because the bees supposedly view the mat as the top surface of their hive from where their combs are hung from and this curbs their tendency to want to build any higher. Not a perfect solution always, but it helps. Using the migratory lids that are basically a piece of plywood placed on top of the hive with cleats on the front and back would prevent any burr comb building, but might be harder to remove if your bees like to use lots of propolis to seal it down.
Simon