My best recommendation would be to use the forum search function and read through the posts -- though I can't say with any certainty that your exact Qs have been addressed. I've never been in you particular shoes so have never needed to look. There is a great deal of info to be found here without folks "reinventing the wheel". Hopefully, what you seek is already here.

Can't help much with the glass Q except to say that aquarium glass is almost always (if not always) tempered glass. My understanding is that as such, drilling is extremely difficult to do without breaking/cracking it.

You Tube is a great place to look at videos of people setting up Paladariums in your case (water + land). People will put a sheet of plexiglas on an angle in one corner to drop the pump into sort of like a sump if you want a water feature and then either fill the remainder with drainage stones then put some sort of weed barrier to keep the drainage layer clear of soil. Then put potting soil on top of that. If you're going to put an animal in there I would make sure the soil doesn't have any fertilizer added. I use the ABG soil - http://www.amazon.com/Joshs-Frogs-ABG-Quart-Gallon/dp/B00JJS9WOO  Then add the plants. I would also use some hardwood leaves over the soil to keep it from washing away, Here's a diagram that should help -

http://www.exo-terra.com/download/high_res/products/images/BioDrain_System_Installation.jpg

In the diagram they use decorative stones in the water part but you could just as easily add a piece of mopani wood to separate the water from land. HTH

I would also add springtails and or pill bugs to the land part they are natures garbage men and will help eat all the detritus from the plants and any frogs, or lizard you may want to add. But let the plants etc get established a bit before adding an animal.