Stage 1 is completing the 309/100 app online (which is the 47SP) and paying then uploading evidence and the sponsor doing their part. Stage 2 is done two years after applying and is the 100 eligibility.
If you've only made the initial application for the 309/100 and you're asking how to skip to PR because your relationship is longer than 2 years with a child of the relationship, it doesn't work that way. You apply for the 309/100 as normal and wait the normal wait times for the 309 processing. A CO will get to your app whenever s/he does and decide whether to grant you the 309 and 100 at the same time, effectively waiving the 2 year waiting period for 100 eligibility due to long term relationship. Note that you should be supplying enough evidence of the length of your relationship and that it is still at the discretion of the CO whether to grant it or not.
If that's not what you're referring to, then you need to try and be more specific as we don't understand your questions.