Generally I prefer to use stripboard, specifically this type with solder mask:
Unfortunately a lot of sellers use the "stripboard" keyword on listing for non-stripboard so you need to do some looking to find the real deal.
That plated through hole board you're using is nice when you want to do a double sided board but it ends up being more work soldering because the holes aren't connected to each other.
I use this tool: https://veecad.com/
It's pretty clunky and not open source but the free version works fine and it is easy to get started with. Professional EDA tools like Kicad are much better but have a steep learning curve
If you put a little thought into your designs the tracks make most of the connections and you just have to add a few wire jumpers where necessary. It's kind of fun to shift things around in veecad to find the most efficient design.
After creating your design, you make the necessary cuts in the tracks. It's very fast and easy to do this at the holes with one of these tools:
It's just a drill bit mounted in a handle so you could easily make your own if you wanted to but they're pretty cheap.
You can also cut the tracks between the holes with a hobby knife but this is a bit more work so I only do it where necessary, such as a 2x3 header where you don't have an extra hole to spare for the cut. The soldermask type of stripboard I mentioned previously does make that a little more difficult but not much more. You can also get the bare copper style of stripboard. The reason I like the solder mask is the solder tends to wick along the bare tracks so your soldering job will look a bit sloppy even when you're being careful.