i moved into my current house with my mom in 1999 and have always felt a weird presence in the upstairs.This presence made me extremely uncomfortable to the point where i moved my bedroom to the opposite side of the house and this seemed to solve the problem but recently i have been hearing weird noises and seeing shadows in all parts of the house and i feel this negative presence not only upstairs but it seems to be all through the house now.

First off, let me say that because you are feeling uncomfortable and have seen shadows does not mean you have a negative spirit in your house. What you might have is what we call a "Personality Conflict" between you and the spirit. You may have a spirit of a former resident who loved the house and wanted to stay there. Then you and your family move in and make changes--even something as simple as different decorations and furniture--and this upsets the spirit because they liked it exactly as it was. This doesn't mean the spirit is negative.
Some things you can try to "claim your space" is to set boundaries. State exactly what you want from the spirit. For example, "This is my room. I don't want to see your shadow in here." or "This is my space in the house. I'd like to live peacefully with you, so please stay in your room on the other side of the house." I tell my clients to be direct, but not confrontational. You don't want to aggravate the spirit. Try to state your boundaries when you feel strong and confident about yourself. You will probably have to repeat your boundaries, but you should begin to see it working if you keep it up. Getting everyone in the house to do the same will help too.
Some other suggestions, since you feel this is negative, is to bring more positive aspects into the home. As they say, light and dark cannot occupy the same space. Try opening windows, curtains, and drapes; letting natural sunlight into the house. If you haven't already, think about having the house blessed. Also, the smoke from burning sage has been proven to release positive ions into the air. In a technique called smudging, you can walk around the house as you burn a clump of dried sage, letting the smoke waft through each room.
If none of these suggestions seem to help, you may want to contact your local paranormal investigative group. Please make sure you are dealing with a reputable group that doesn't charge you for their services. Links for some groups can be found on our website at: http://www.southjerseyghostresearch.org/links.htm or on The Shadowlands: http://theshadowlands.net/ghost/links.htm