So I have a Galaxy Note II and recently rooted the device for the main reason to overclock it. I want a faster web browsing experience. I installed the App. Set CPU so that when I have either Google Maps or Chrome running the CPU settings which were at a default range of 200 MHz to 1.60Ghz to be bumped up to 400MHz to 1.60MHz. Will this damage my phone? I can feel a tangible difference with the slight bump up. Will this overclocking degrade the phones chips??
To directly answer your question: no, this modification will not harm your device.
To elaborate: You didn't overclock your device (that's why I said it was safe). You raised the minimum frequency. What you see in Set CPU is the scaling range. For any given moment your device decides which frequency it needs to do what it's doing.
For example when only reading and not scrolling it needs only 200 MHz to basically wait for further input. This is done for better battery life. When actively loading pages the device will automatically increase the operating frequency up to the limit of your scaling range. This increases performance, but is worse for battery. In both of your cases the maximum scaling frequency is 1600 MHz. You told the device to save less power when idling, but kept the maximum "speed" the same.
Overclocking on android is done by raising the scaling range maximum value above the default. For example a very small and usually OK overclock for your device would be to set the scaling range to 200MHz to 1700MHz. This modification however can harm your device, but not very likely. It also often requires custom kernels to be flashed. When things go wrong with overclocking you can see random reboots and freezes, and almost never any permanent damage to the device. I suggest you try to read more about this topic on sites like xda-developers, before doing anything else with the device.