You are new to Aikido, but just to say that Aikido is not onlly defensive, but also offensive, with attack from Sh'te/Tori/Nage against Uke (at least we all agree on that term)!
Also, Jodo does include Jo and Bokken, but with Tori (I hope that is still the true term for all) using the Jo to defeat Uke, who is armed with the Bokken.
Someone will probably tell me now that their school practice the opposite as well, but that will not be the way of the Jo!
Don't keep them seperate, you have to find a way so that they compliment eachother. As my late teacher (Sensei Ted Stratton) said, "You can't climb 2 mountains at the same time!"
At the Shudokan Hombu dojo in Seremban, the late Sensei Don Draeger used to teach Jodo to the Aikido students there (who practiced Yoshinkan Aikido).
If you approach your Aikido and Jodo training from the same perspective, you will have no problems. I approach Jo and Bokken training from the same Kamae as I have in Aikido - 60% on the from foot, 40% on the back, centre above the front heal, heals in line, hips square, hands in centre. Same with striking arts.
That is the basic and basis of training, then you also have variation, but that is not the way to learn the art. If you approach both from the same perspective you will improve and build your base in both arts. If you try and keep them seperate and you will only be as good as whichever one you are weakest in.
Give it a go and treat it as Aikido.