Including own logic to sopc system

If you want to use IOWR and IORD, the simpliest way to add Microcontroller peripherial to you NIOS system in SOPC editor. I think you better to use unidirectional ports, so input or output only. Good idea to utilize the interrupt system of NIOS at IORD.

Another way is to create your own components using Avalon MM slave and master interfaces. Templates are available in the menu of Component Editor. In this case you will need to apply conduits too, so after you added your Avalon MM interfaces, add a CONDUIT too, and create the signals for this interface too. A simple example.

You have one Avalon MM slave interface with 32 bit wide data signal input, then create a conduit interface too, then a conduit signal same wide as your data, but as output. After you succesfully built your NIOS you will see the pins of this conduit in the schematic diagram.

Do not forget to always add the handshaking signals too, like ready, dataavailable, waitrequest, etc. Anyway, Component Editor will make noise to you if any HS signal is missing.