If the light coming through the window is strong, position a sheet of white card on the opposite side of the subject to the window. Light will be reflected back into the shadow side of the subject. Altering the angle and distance of this card gives you considerable control over lighting effects.
Elephant Hawkshead Moth, You Connect member Dean Powell, Canon PowerShot G5
A sheet of white card can also be used outdoors when photographing small subjects. It is surprising the effect this small reflector can have. It does not need a stand – just hold it near to the subject (but outside the lens field-of-view) as you take the picture.
Using the built-in flash on your EOS is generally not recommended for close-up photography as the flash can be too powerful for correct exposure. The distance between the flash and lens can means that most illumination goes over the top or to the side of the subject.
Try using one or more Speedlite flashes off an EOS camera, either with the Canon Off Camera Shoe Cord or the Speedlite wireless system. This allows you to use the flash unit further from the subject than the camera to help the exposure, and you can angle the flash head so that the illumination reaches the subject. A single Speedlite, plus a white card reflector, can create excellent lighting for the subject.
If you do have to use the built-in flash, try to enclose your subject with white card on three sides and above. The flash reaching the subject will also be reflected from the card, softening and diffusing the light.