You have to understand that the process of upgrading an OS on a network device doesn't overwrite the existing configuration. You are only upgrading the OS image file. The device configuration is a separate entity than the OS image file. You will not lose your existing configuration as long as you save it to the startup-configuration which is stored in the NVRAM.
The only thing you will need to reconfigure in your running configuration after you have uploaded the new IOS image to your network device is to point the startup configuration (by editing running config and saving to memory) to the correct IOS image (the new OS image that you uploaded) stored in Flash memory to be used when the router or network device boots up. You will have to reboot the network device to start using the new OS image file.
The command in your running-config to point to the new IOS image should be something like the following and may differ based on the type of Cisco IOS or hardware platform used:
boot system flash bootflash:[name of image file].bin
A Cisco IOS network device has the following memory types that store various software programs, images and permanent or transient control and forwarding information used by the network device -
NVRAM - Is a read/write memory type that stores the start-up configuration, as the name indicates, its a non-volatile memory type which means that the information stored in it is not lost after loss of power to the NVRAM chip i.e. a device reboot
Flash (also referred to as bootflash) - Also a non-volatile read/write memory type that stores the current Cisco IOS image in use (that loads during router bootup) and additionally can store more IOS images to be used as alternatives
ROM - as the name suggests its a read only memory type memory i.e. you cannot write to it and can only read from it, it stores the POST (power on self test) diagnostic software and the bootstrap program used during boot up process of the network device to check for hardware issues, and is again a non-volatile memory type
DRAM - is the only volatile memory type that stores the running-config and other control plane and forwarding plane information such as the routing table, the adjacency table, NAT translation table, etc. The information stored in this memory is lost on loss of power i.e. a device reboot and the network device has to repopulate the information again using various discovery mechanisms and application code (i.e. using the OS code and startup-configuration which are stored in flash memory and NVRAM respectively)
