Upgrade Marlin firmware

I build , Repap Prusa i3, printer about 3 years ago. I would like to upgrade my Arduino IDE from the old version to the new version on my , auduino Mega 2560 board. Can I just upload over the version that is on the now or how would I go about doing This?
I also would like to upgrade my Marlin Firmware from the old version to the new. I need to do this because of the new all metal Hotend to do the configuration of it. Again can I upgrade (upload) over the old or not?
If I can upgrade (upload) over the old will have to redo my configurations again?
ED

Arduino IDE runs on PC under Windows / OS X / Linux
You can load and install the latest arduino IDE, drivers, libraries.

Do you have a copy of your existing Marlin running your printer.

No -- you can't download firmware from printer arduino -- it would be compiled code

Certain parameters are set in the configuration.h file of marlin to setup for
specific printer configuration.
The configuration.h file is pretty self explanatory

Set up configuration.h ---- compile, upload --- new Marlin firmware

Do I have to reset the board If I use the same Arduino version I have now, but use the new version of marlin ?

Are you asking if you have to reset Arduino before loading the new firmware? If so, no, you don't need to. It is going to overwrite the new code and reset itself when the firmware is uploaded.

Be very very careful when modifying configuration.h .It isn't very complicated but can be intimidating and get ready for some failed attempts and unexpected behaviour from your printer, as there are many options (new ones are added each day).

Edited 1 time(s). Last edit at 02/04/2017 01:46PM by drmaestro.

It sound's like you do not know how the arduino and ide communicate.
Spend some time reading up on the arduino and you will realise how easy it is to modify and upload new versions of marlin.