Programming of Microcontrollers and other peripherals
You asked to "Please explain in simple terms." so I will do thus that and omit all the technical details.


  Once we write the software code for the microcontroller in our PC, how do we load it into the microcontroller?


Most manufacturers have a special 'box' which can be connected to the microcontroller  with a 'programming cable'. The box connects to you PC with USB. The cable connects to certain pins of the microcontroller. The price of the box varies a lot and can be as little as $15 or as high as $250. You can also use the box for debugging, stepping through the code, setting breakpoints etc. 


  How is the TFT information (transferred to) stored in the SPI Flash initially?


Most likely you have to write a program to upload the data into it. (Just like you have to write a program to get the data out of it).

There are two other possibilities:


Program the chip before placing it on the PCB. 
Sometimes it can be programmed in-situ (on the board). But for that you may need a special circuit on the PCB to make sure you isolate it from the microcontroller which it is connected to. You will also need separate SPI programming hardware. 



  Does microcontroller have any sort of bootcode initially?


Some do, some don't. It depends on the type and the manufacturer. 



In a comment you asked:


  Thank you very much for keeping this answer as simple as possible. Can you please tell the name of the interface which is used to load the software code in the microcontroller?


The interface differs per manufacturer. 

Some use JTAG (ARM) or the JTAG pins with a non-JTAG protocol (ARM SWD) Others use the SPI interface (ATMEL).  

However many have their own interface and have a proprietary protocol. Especially on chips with a very low pin count, (e.g. 6, 8, 14, or 16 pins) they use a one-wire debug interface.

Most often the protocol is unknown but some have been disclosed and other debug interfaces have been reverse engineered. The latter especially with the more popular chips.

Just as a side note: when you are new to working with micro-controllers it is worth every penny to buy a ready-made box. Even with that it is difficult enough to get the interface and the chip up and running.