Hi @bsen2018!
Yes, the only exception will be the q2studio application icon will keep using the old version (2017.10), but it doesn't look like that will be an issue for you. Check out this post for some instructions.
Do you plan on doing any analysis with DADA2? If so we want to use those directly (forward and reverse are denoised independently before being merged). Otherwise there's no problem starting with your merged sequences.
It does look like you have the paired-end sequences more or less sorted out though, so I would use those since you have them.
The --type argument just needs to be swapped from SampleData[SequencesWithQuality] to SampleData[PairedEndSequencesWithQuality] otherwise what you have looks great!
Let me know if you run into further issues!