@Sunny27 - My husband and I own a company and we pay quarterly. However, I'm also employed as a freelancer and work with a W-9 or on a 1099 at the end of the year, so we as individuals file at the end of the year as well as quarterly for our business. When we file quarterly, we itemize all of our business expenses, which helps a lot to offset the taxes owed.
Aside from that, I itemize any expenses I can for my freelance work (within reason) and we almost always end up taking the whole mess to a professional. It tends to get a little confusing so my suggestion is that anyone working for an employer that does -not- provided tax withholding is to go ahead and take care of it with a professional. Otherwise, you might be in for a ride!