Here is an easy way to line up your properties in Clash of Clans so that upgrades are a piece of cake. Doing this will make it easy to see what is left to upgrade before you start that town hall upgrade and also easy to see what properties have just finished building.
The important thing to note is that you can keep your home village setup any way you like. Here is my current farming base for example and as you can see with lots of properties it is quite tedious to keep track of which properties need upgrading and which are fully upgraded for this town hall level.
Thanks to a recent update we now have the option to setup multiple layouts for our village. What I recommend doing is using one of your village layouts solely to keep track of your upgrades. I never actually set this layout as active, I only use it as a place to organize my properties so I can checkout my upgrade progress at a glance. Technically you have six layout slots to choose from here because it doesn't matter if you use the home or war slots, so you should still have plenty of room left to play with your normal layouts. In this example I used my second home village slot to track my upgrades as you can see here.
The nice part about this setup is that once I get a builder to start working on a property upgrade I will move the property into a "currently upgrading" area. This way when the builder finishes I notice at a glance and move it to either the still able to upgrade area or the upgraded area it belongs to. Properties which cost gold to upgrade get moved to the gold zones, ones that cost elixir move to the elixir zones and of course the properties that require dark elixir to upgrade land in the dark zones.
The properties always get moved around as they upgrade, always trying to keep my builders busy in the currently upgrading zone and slowly moving all properties over to the upgraded side as they get to the point where they need a higher town hall to continue. With this process over time my three "upgraded" zones and my three "upgrades" zones flop from side to side. Each time I upgrade my town hall the zones start again on the opposite side as they did with the previous town hall. My town hall always stays on the side which has items waiting for upgrades because it is typically always the last property I move across.
I was really glad when the update to allow multiple village layouts came out a while back because I knew I could start getting super OCD with monitoring and optimizing my upgrades while not having to worry about people attacking a weak base. Actually what I use to do before multiple layouts were possible was to tap the button to remove all my properties and then scroll around the slider at the bottom which groups all of the properties by type and level. It was always super inefficient and frustrating to keep track in that way.
The workaround described above that I am currently using is pretty efficient and kind of fun to use. I would really love for Clash of Clans to incorporate their own solution to this as a part of the game. I doubt they will ever think about it, but some way of being able to list pending upgrades for your current town hall level would be very handy. Until then, this is my process.