In any application of watermarking, the selection of feature vectors from a given multimedia content is important from the perspective of robustness and security. In the case of PDF document, the spaces between words and characters are commonly utilized for embedding watermark in the conventional schemes. Instead of modifying the space values directly, researchers proposed to manipulate the frequency components of the space values by using the quantization index modulation (QIM) watermarking method. The QIM method is further combined with dither modulation (DM) to enhance secrecy of watermark. In this paper, we improve the imperceptibility of watermarked PDF document by investigating into the DM operation. The proposed method selects the best secret key among some candidates which minimizes the degradation caused by embedding watermark. Information about the selected key is also embedded as side information so that the embedded watermark can be extracted without referring to the original PDF document. The degree of distortion caused by watermark embedding is quantitatively measured in our experiment. It is verified that the gain in terms of signal-to-noise ratio in the proposed method is increased with the number of secret key candidates.