Hello Steffen,
EDIT: I just found this excellent chimera checking tutorial written by Greg. Definitely start there.
You can run uchime-ref at any time, so it's probably best to do it late in your pipeline, when you have fewer features to check. Say after step 3.
Uchime-denovo requires size annotations, so you have to run it after step 1 (dereplication adds size annotations). I have seen people do uchime-denovo before or after clustering (or both!). Greg recommends running it after clustering.
The uchime de novo algorithm is slow, so running it after clustering saves some time. (Actually it's pretty fast but not easily parallelizable, so it's seems slow!). Running it before clustering may improve accuracy because there are more parent reads that can explain and detect low abundance chimeras.
Let me know if that helps,
Colin