Hi @iuliachiciudean,
This really depends on what you are planning on doing with your data. If you are planning on using DADA2 to denoise your sequences, then you shouldn't merge your reads here, DADA2 will do that itself.
If you are planning on using Deblur to denoise your reads, or OTU clustering, then you are right to merge your reads first, but even then it is recommended that you ensure your sequences have gone through some sort of quality filtering step first. Check out this example for example in Moving Pictures tutorial.
As for what the red texts mean, check out this detailed explanation of the quality plots and let us know if you have any remaining questions. Thanks and happy :qiime2:'in.