It usually just flows when I pet and cuddle them without any effort on my part. I know if my hands get hot the pet in question *really* needed it as the hotter my hands get the more energy is flowing. If I know they have a specific issue going on I will consciously aim the energy for the first few breaths by focusing on sending to the area or by thinking something like "Reiki on the arthritis". Reiki in general is harmless. Hurting someone with it is like trying to concuss someone with nerf. Now IMO some people accidently send their own personal energy along with the Reiki and so may not be appropriate for the person or pet in need. If you (or reiki practitioner) are mentally pushing at the energy personal energy is more apt to be sent as well as the Reiki. Just try to relax and trust the Reiki energy to flow where it is needed at the appropriate rate.
Reiki_On
http://groups.yahoo.com/group/Reiki_On is a free teaching group that offers free attunements to both humans and animals in Reiki I & II. I got my first attunement though them and signed up all of my pets though not all accepted. I highly reccomend attunements to anyone interested in Reiki. It is easy to learn and the more you use it the more oomph it has.