Hi,
I didnt use Pu/Pd until my lo was older. I found he never really needed it until he started to stand up in his crib. When this happened, everytime he stood, I would gently lay him down and repeat over and over "It's just bedtime". Eventually he would tire and then stay down. But in this case he was never crying, he just wanted to play- but it was past bedtime so that's why I used it.
I, like you, found that when my lo was upset Pu/Pd made it worse. Instead I stayed by his side and kept my hand on his back to let him know I was here with him. I would repeat over and over " Mommy's here, It's just bed time, Shhhhh..." until he would settle. Sometimes I had to stay 30-60 minutes. I didnt leave the room until he was sleeping. Now this was when he was little (4-7 months).
After establishing that, one day I found when I put him to bed he was fine. I could leave the room. He felt safe! It was really great for 2 months. Then just now it got where he would cry when I leave. That's when I thought ok- what's going on (teething, separation anxiety, all of the above?) So, I went back to staying with him but leaving as soon as I felt I had stayed all I could or I felt he would be fine. I would wait outside his room and if he cried for more than 5 min. I went back in. I would always tell him, mommy will be right back and I actually followed through.
Now, that lasted 2 weeks and he is ok. He is back on track (at least for awhile). What I learned is that everything is temporary - they go through stages. You just have to reassure them and be there for them when they are upset. Dont worry about it becoming a habit because once they feel secure then they should go back to sleeping fine on their own.
I hope this helps. Also, consider if you are doing anything different in your bedtime routine that may be upsetting your lo? If not, then dont worry. Stop the pu/pd if it is upsetting your baby and you. Just go with the hand on the back and not leaving baby's side until you feel safe to do so. Also, when you do go in and do all this- go in without getting upset or frustrated. Just accept that baby is having a hard time and you will be there to help him/her through it. If you are relaxed then baby will feel relaxed too. I found when my husband went in, baby got more worked up. Unfortunately, I had to do all the bedtimes for what seemed like the longest time but that's the way it was. It really wont last forever. Hope you feel better soon.