Well, of course it all has an effect on the rest of Liferay as well. Liferay provides quite a bit of the HTML DOM of your page, and if you change the presentation of all of those elements, you'll have to take care to style Liferay's elements too.
Is this a conflict? No. Let's go for the simplest case: You declare div {color:green;}. Of course, now everything, your components as well as Liferay's components, use green text. If you only want to style your own portlets, you might want to specify some portlets: div.portlet-my-own-application {color:green;}
I know that color is a too simple usecase, but I hope it illustrates the solution strategy.
Rather than following Artem Khojoyan's suggestion to override Liferay's base.css, I'd recommend to take a look at the resulting css, what's effective etc., and simplify your own css - adapt it to be used within Liferay - by inspecting the effective CSS for every elements that looks off. Firebug or any of it's relatives are your friend.
I'm afraid, with the details "I'm doing something which has an effect on Liferay UI" there's nothing much more to help you. In fact, I'd hope that what you do has an effect on Liferay's UI... You'll just need to find the proper CSS code