From what you are describing I assume you are talking about custom firmware running on a processor that is talking directly to the DWM3000 radio module over SPI. If that’s not what you are doing then ignore these answers.
Does each anchor need it’s own microcontroller in order to sync up the clocks?
They will all need to be connected to a processor. The DWM3000 is a dumb radio module, it needs a processor to control it. You could in theory connect several to the same processor but generally that makes life more complicated. It’s far simpler to put a separate processor on each module. This also makes things simpler mechanically since each radio is a self contained module.
What IDE is best to use for configuration of each tag?
Whatever works best for the processor you are using
Do we need a linux machine?
No
How does the GUI and API work?
If you are working in the way I think then the GUI isn’t applicable. You are writing firmware to drive the radio. If you want a GUI you need to write it.
The API gives you a series of function calls - Configure radio, send packet, read packet, get packet receive time etc… that you can use to measure ranges. Normally the first stage is to create a measure range function that uses API calls to talk to another device and get a range.
Where do we get started?
First download the source for the API and port it to your processor (mainly change the SPI read/write functions to work on your hardware).
Then look at the examples included with the API, they include both sides of a Two Way Range system, this is in effect a pre-made version of the get range function mentioned above. Get that working and measuring ranges.
Then expand the example to include the ability to include an ID for the device you wish to measure to so that you can measure ranges to multiple devices in a controlled way.
Once you are there you can measure your 4 ranges and calculate how far off centre you are.
These steps are common and there will be lots of posts here already from people doing similar things.
The DW1000 app notes will give all sorts of information on how to improve accuracies and get the best out of the system, these are almost all equally applicable to the DW3000.
Why did we choose such a complicated sensor?
Because you enjoy suffering?
There is a simple out of the box positioning system for the DWM1001C called PANS. I believe there is also some fairly out of the box hardware/firmware for the DW3000 and the iphone localisation system. As soon as you get outside those it does get complicated. Getting the radio up and running on new hardware is a low level firmware task, nothing that hard technically but very intimidating and a steep learning curve if you aren’t familiar with it. After that getting rough ranges is relatively simple. Getting accurate ranges and positions is complicated.
But if you get it right they are capable of getting very good results.
In terms of your specific application on the plus side if you are simply trying to guide a drone in to the pad then you don’t need position, you just need to get all the ranges the same and then reduce them all at equal rates. On the down side you are dealing with a dynamic system where things are constantly moving. Depending on how quickly you can measure ranges you may need to allow for the fact that your ranges aren’t all measured at the same time.