Hi Greg,
With 90mm of aperture you will definitely be able to see the brighter deep sky objects. My first scope was 90mm aperture too (Meade ETX90EC).
Some helpful advice would be to make sure that you try to locate deep sky objects when there is no moon out, and if possible, try to get away from the city lights. With a small aperture you need to make sure that you eliminate as much skyglow due to the moon or city lights as possible! Also, make sure you let your eyesight adapt to the dark, and learn how to use
averted vision
Colour filters won't make any difference when looking at deep sky objects, although some can certainly increase contrast on planetary features.