How many yards have you got? If you are a new weaver, I would recommend to just go with how you have beamed the warp. If you are more experienced, you might be able to adapt the threading or treadling to get the weave pattern you desire. I have unwound a 3.5 yard warp once, and rewound, but you probably need help. The lease sticks need to keep the cross. The warp needs to stay neat. Then switch positions of your 2 sections. If I understand you correctly. What ever you do to rectify your situation, or instead, go with the way things are now, it is a journey of discovery. Don’t worry too much, as you will learn so much.