One of the most important ways a rider or trainer will communicate with a pony is through the action of the reins, which (except for side reins) facilitate communication between a trainer's hand and the pony's mouth. The action of the bit can be very gentle or exceedingly severe depending mostly on how the trainer uses her hands and to a lesser degree on the type of bit used.
Generally, a simple rubber bit gag (straight mouth rubber snaffle) is a good starting point if either you or your pony is just getting started. Start by putting on your pony's bit (and bridle if he wears one). While the bit should not be overly tight, it should fit snugly in the pony's mouth so it is not moving around when he is moving, which can obscure more nuanced rein aids. Personally, I find a bit that is a little bit too tight more preferable to one that is too loose for this reason.
Once your pony is wearing his bit and bridle, attach the reins to his bit if you have not already done so. You will want to begin by taking up the reins (I will assume you are on ground and behind your pony) and keeping gentle contact with the pony's mouth. It is a good idea to get in the habit of always maintaining some (gentle) pressure on the reins. This is somewhat analogous to always keeping your hands on the steering wheel of your car even when you are not turning or making gross corrections to your path of travel. In this way, your will minimize confusing your pony and your rein aids will be smoother.
You have taken up your pony's reins and have some contact with his mouth at the halt. Now, cluck with your tongue (or tell him to "walk on") accompanied by a flick of the crop or whip, with a slight easing of rein pressure - still maintaining some light rein contact. This indicates to your pony that you wish him to move forward. He should begin walking. If not, you will want to try clucking again and apply a harder swat of crop. This might be necessary the first few times if the pony is not accustomed to having any rein contact while moving forward. Repeat this as necessary so your pony understands you will keep some contact with his mouth even when moving.
Cool...your pony is moving forward and you have some contact with his mouth! Now it's time to stop him :) After a couple steps forward, say "whoa" and start increasing the amount of rein contact. Apply the pressure evenly to both reins, and steadily increase it until he stops, at which point ease the pressure on the reins back to the amount you had before asking for the halt (do not release all contact on the reins - you should always keep some light contact). Repeat this procedure a few times for him to learn to yield to increased rein pressure and come to halt. Using the verbal command "whoa" will help with this.
Your pony now understands how to halt through rein aids, so it is time to confirm that he knows how to stand properly at the halt. Tell your pony to "square up." As discussed previously, this will indicate to your pony you wish him to come to come to attention and stand properly. Make sure this is the case: take a look at how your pony is standing to ensure he is at attention with legs square, head up, etc. If not, use your hands or crop (lightly) to position his body correctly. Once you have it positioned correctly, wait a few seconds (10 - 30 seconds), then have him take a step or two forward. Again you will do this by saying "walk on" accompanied by a swat of the crop, while still maintaining light contact on the reins. When he has taken a couple steps forward, stop him. Remember to stop, say "whoa" and steadily increase the amount of rein contact evenly over both reins. Once he is back at the halt, again say "square up" and check his position. If necessary, correct his position with your hand or crop. Repeat this procedure until he learns so come to attention and stand properly when you say "square up."
When your pony will halt and square up properly every time you ask him, it's time to teach him to back up. At the halt, begin by clucking your tongue and increasing the pressure on both reins evenly. You may wish to use a voice command such as "back" to reinforce this. It may be easier to alternatively apply and release pressure on the reins rather than constant pressure. Once your pony has taken a few steps back, release the excess tension on the reins and let him know he was good.
To steer your pony right or left, start off at the walk (from the halt, start your pony walking with a light flick of your crop and either clucking or telling him to "walk" or "walk on" with a simultaneous slight easing of rein tension) and give a gentle increase in tension in one rein or the other not both. Apply more pressure to the right rein to steer your pony right, or increase pressure on the left rein to steer your pony left.
To indicate to your pony that you wish to slow down the pace, you can increase rein pressure across both reins evenly while using a verbal cue such as "easy" (do not use "whoa" unless you are looking for a full halt, also "slow" sounds enough like "whoa" that it can confuse the pony).
A half halt can be used to refocus your pony's attention back to you. Moreover, it can assist in rebalancing the pony if he is not carrying his weight correctly or is otherwise getting off balance. You can apply a half halt by increasing rein tension evenly on both reins, and gently flicking your crop on the pony's back. This should communicate to the pony you wish him to slow, rebalance, and move on in the gait. This is also useful when preparing to make a transition between gaits.
Just like riding a bio-equine, training your pony should be fun. You might want to try using blinders, or even better a blindfold or sensory deprivation type hood which still allows you to use a bit. This will help your pony concentrate on your rein aids and adds a nice dimension to the play.
Once your pony understands (and correctly responds to) your rein commands, it is time to teach him leg aids.