Evesta, I see some things you have done your homework on but I see some issues as well. This is from personal experience First off, The bog garden, The bog garden itself with no filter and as a waterfall is not a great idea, first off the water will run past the plants faster than they can filter. Good plant filtering is best done with slow water movement. Not that it can't be done, Good plant filters are plants like anachris, hornwort, lettuce, hyacinths, and parrot feather just to name a few, most will grow with roots being exposed in the water column, lilies, marginal plants, and bog plants that grow above the water and the roots grow deep don't do as well for filtering but will do some. But what you are trying to do will work to a great degree, simply split off the primary flow of water to a primary waterfall and divert with a valve a line to the bog garden and slow the water down passing thru it. I would recommend about 1/4 or slightly less of your total pumping capacity.(2400gph = 600 gph thru the plant filter) The rest going to the primary water fall.
Placing valves is a little trickier because different scenarios require different placement of valves, In your case I'll simply say I would put one before and after the pump WITH quick disconnects! This will greatly reduce headaches when you need to replace pump! And you will need to sooner or later. Also with having a valve before and after it makes adding a Tee later to divert water a lot more simple. Now plumb your lines to what you need water to go to, the valves for them to me the closer the better in my opinion when you can. Also for your drain/ dump valve, make sure it is at the lowest spot in the piping system so you can clear the lines out of settlement when you need to work on bog garden, or waterfall etc This can be tied in also with the valve coming from a seperator from the bottom drain. Last but not least. Look for the best place to put/hide a filter box,UV light, (I'm not saying get one at this point but it is far easier to plumb in a Tee and valve for later use just in case!) Put that valve facing in the direction of the optional filter UV light location that would best work and is in line with the pump. I would rather plumb with the thought ahead of what I might need and get them in place on the install. Installing valves after the initial install can really be a pain if your already landscaped and no room to maneuver piping. I would recommend really investing in a filter fall unit, for the money it's relatively cheap, very efficient and makes starting a water fall A LOT more easier to start with!
I use the filter falls with biol balls and three different grades of Matala filter, and Matala course pre filter in my skimmer box, no bottom drain but I assure you the next KOI pond will!!! I have a lotus planted in a 50 gallon tub and and pump 1/4 of my ponds return water over it and into a Planted only 300 gallon pond which then waterfalls over into the primary pond. 1/4 of my return is piped so it pushes water from the far end of the pond to the skimmer, 1/2 of my water is returned through the filter fall filter and down a 25' stream waterfall. My 15 watt UV light is plumbed into the return line going to the lotus and plant area, the other 15watt UV light is in my savio skimmer, That is not the best place or idea in my opinion but that is the way Savio sells it and it does work to some extent.