What is the best way to customize bootstrap/override settings?

One of my biggest frustrations is trying to set properties that aren’t set with bootstrap. For example, I want to change the navtabs to not have a solid 3px border around it when clicked. I’d also like to put a border around the sides and top of the tab to give my navtab content areas a bit more distriction. For example:

There are several times I want to modify a attribute for an element but I am unable as it’s locked for Bootstrap:

image

My question - can I just simply disable this? I don’t want to be constrained by this. I would like to be able to override this as I see fit. Is there any issue with doing so?

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