Try to arrive 10 minutes before all events. If you arrive prior to the beginning of a group of sits, you can enter the zendo whenever you wish. You should enter with your hands in gassho and briefly bow to the altar as you enter. Take the next available place closest to the altar. Walk to your place with your hands still in gassho, and bow to the altar again, then bow to the place across from you before sitting. You should settle into your zazen posture before the jikijitsu begins striking the bell.
You should never enter the zendo while a sit or service is in progress, or leave before it is over, so that you don't cause a disruption. If you arrive during a sit or service, you should wait outside the building until you hear the bell and clappers announcing the beginning of kinhin, then quietly and discretely enter, remove your shoes, and join the end of the kinhin line. If the weather does not allow you to wait outside, you can enter quietly and sit in the shoe changing area until kinhin begins. Never enter the zendo and take a seat while a sit or service is in progress.
You should sit still in the zendo. If your posture is good, the only voluntary muscles that need to be (mildly) engaged are those that hold your torso erect. Don't join a sit late or leave the zendo during a sit. Don't change positions, stretch, scratch yourself, blow your nose, etc.
It may be difficult to sit still at first, but you will eventually find that it's essential to your practice. If your body is not calm, it will be extremely difficult to relax your mind. If the mind is anxious, the body will be tensed, and the tension will lead to pain and fatigue. You have to let the one feed the other until you reach the state of "body and mind fallen off".
Some allowances can be made for people who are new to the practice. If you absolutely must move, do so as slowly, quietly, and discretely as possible. When you sit in the zendo, you are not only cultivating your own practice, but supporting the practice of everyone around you, so you should cause as little disturbance as you can. Most importantly, be aware of the difference between a genuine need to move a part of the body that is in pain and a desire to move which is actually an excuse to run away from boredom or other mental discomfort, instead of confronting it and sitting with it.
If you have to cough, cough. You'll probably make more of a disturbance trying to suppress a cough than you will by just coughing.
Be mindful of the effect of the things you bring into the zendo with you. Put your shoes, coat, and umbrella in the appropriate places. Stow your personal belongings away neatly so others won't trip over them. Turn off your cellphone, pager, and other electronic devices that could make noise while you're sitting.
Dress conservatively in neutral colors so you don't attract attention, and don't wear strong perfumes. Take off your watch and put it in your pocket. The jikijitsu has a clock which he or she will use to keep track of the time. Watching the clock is just a way to avoid your practice. Take off any jewelry that you would normally fidget with nervously. Don't make hand gestures or chant during zazen. Remove all the devices that you use to distract yourself from the work you need to do. When you sit, sit.