HELP for ddRAD de novo map analysis

I’m new on Galaxy and NGS analyses. I need some advices and, if available, a tutorial would be grate.
I’m working with ddRAD data, starting from demultiplexed fastq file provided by sequencing service. Then I have two files from each sample (R1 and R2). In tutorials that I found paired ends are not considered and de novo map was performed only using r1. Moreover, I read that in current stacks version on Galaxy it is not possible to analyse paired-ends directly.

How can I analyse paired-ends reads indirectly?
I thought to join the two reads using FASTQ Joiner and perform de novo map on output, but I’m not sure that this is the correct methods.

Are quality control and cleaning better to do before or after the merge?

Hoping for some good advice
I thank you in advance.