The first step is to wash your hair. The protein will penetrate better on very clean hair. If you low poo, it would be a good idea to low poo before a protein treatment. Honestly though, I've washed my hair with a cowash and washed my hair with a low poo before a protein treatment (PT) and I don't notice any difference.
For your first PT, please test a small strand/section of hair. Protein treatments aren't for everyone. It is better to have a small section of hair that is rough and hard and craving moisture that to have a whole head of awful.
After washing, towel dry your hair and add your PT. Towel drying helps prevent the water on your hair from diluting the PT. The longer the PT is on your head, the more protein will penetrate into your hair's cortex. It is best to follow the instructions on the bottle the first time you use that particular PT. After that, you can experiment with leaving a PT on longer, if you think your hair needs more protein. Some people (me) leave PTs on for an hour.
Rinse and towel dry your hair again. At this point, your hair may feel just fine. It may also feel hard and awful. This is also normal. After my first PT, before adding the DT, I thought "Welp, I broke my hair." My hair felt hard and awful. Adding more moisture should make your hair feel nice again. Towel dry your hair and add either a deep treatment (DT) or a moisturizing conditioner. If you add a DT with ingredeints that can penetrate your hair's cortex (coconut oil, olive oil, etc.) you can leave the DT on up to an hour. Rinse and style as usual.
If your hair tends not to need much moisture, and you are using a moisturizing PT (Spiral Solutions Repairing Protein Treatment, Ion Effective Care, etc.) you may not need to follow your PT with a DT. If your hair feels fine after the PT, you are good to go. The first time you try a PT, you should follow with a DT or moisturizing conditioner just in case.
Curltalk's Rymorg posted a thread on how to do PTs and DTs. Rymorg is a stylist who trains other stylists. There are lots of good tips in the first post and throughout the thread. Many of the tips were repeated in this post.