I concur that different dojo's will have differing etiquettes. Hence naturally the correct etiquette will be to follow your instructors example.
I am currently training in Iwama, Japan under Nemoto Sensei. This is the etiquette as he explained it to me, (happens to be the same at my home dojo too). Realize it goes a little bit further than a simple Seiza Rei, but it may be of interest to you.
Place the Bokken, blade towards you, with the tsuba on the left hand side. This is the hardest position to draw the blade (If you are right handed !).
Kneeling bow to your partner at the start of practice:
Place the bokken right side, curve facing in, tsuba to the front. (Neutral position)
Kneeling bow to your partner(s) during practice:
Place the bokken left side, curve facing in, tsuba to the front.
(ready to attack)
Kneeling bow to your partner at the end of practice:
Place the bokken right side, curve facing in, tsuba to the front.
Place the bokken, curved edge towards you, with the tsuba on the left. (Neutral position)
Holding the weapon during practice:
Hold the weapon at your left side with the curved edge up.
Holding the weapon before and after practice:
Hold the blade at your right side with the curved edge down. Least offensive position. (Neutral position)
With the ken at right side. Lean the body forward but don't tip the weapon forward. (Do this with a real blade and watch the shock-horror as you drop the weapon on the floor, which is also why they place their thumb on the tsuba).
Drawing the blade out into ken-kamai:
I have had two ways explained to me, the first is to draw the weapon as if it is in a saya. The second is to just "present" it into position.
We always bow in and out with our weapons at the start of class if we know we are going to use them. If we take weapons during practice we do a standing bow to the Shomen. Raising the blade to eye height and then leaning forward. You do this to any new weapon that you practice with, say somebody hands you a tanto for instance.
You should never step over a weapon. You should never lean the ken on the floor as a crutch.Basically treat it with the respect you would if it were a live blade, obviously its not, but treat it that way. Never grab the bokken with your fingers touching the blade side, especially in tachi-dori. (If you are holding it at your side, fine you assume it is in its saya).
Some dojo's they do a mini bow of acknowledgment every time they pass the weapon to one another (I choose to but not everybody in my dojo does)
The final thing I'd mention is that I consider most etiquette to be like a door. That is to say, if you open it, shut it, if you shut it, open it.
If you draw the blade one way, put it back the same way, don't mix things up. If you bow in with the weapon then bow out with it too. I always get a sense of something not being quite right when the door is closed before it was opened, or opened and not closed.
Whatever the form that the etiquette takes, the most important thing is that it is done with sincerity and genuine intent Which sounds like you are doing and thats the important thing !!