Note that there are many tools that you can use for every single step in this general workflow, and you may decide to choose one tool or another depending on many factors. E.g.:
- The type of data you have (e.g., nucleotide, amino acid, codon data, morphological discrete/continuous data, recoded data, etc.).
- Restrictions you want to apply to keep sequences in an alignment (e.g., % of missing data allowed, number of codons/orthologs allowed, minimum number of taxa in an alignment, etc.).
- Biological question you want to ask (e.g., does concatenating/partitioning my sequence alignment affect X? Do you want to test the effect of different priors on Y? Do you want to check the effect of taxon sampling and how this may affect Z? Do you want to account for ILS, coalescence,...? Do you want to benchmark different tools for task W? Etc.).
- And many others...
To this end, it is very hard to say use X or Y tool for a specific task; every researcher may follow a specific pipeline they have designed or has been already set up in their lab. It is not right/wrong using one tool or another, concatenating/partitioning your dataset, using the species/consensus/gene trees, etc. If you have somewhat followed the general workflow, you have applied the filters you could think of to "clean" your data (and can justify them and provide instructions for other people to reproduce your results without problems), and are happy with the sequence alignment and phylogeny you have inferred because you can test your biological hypothesis or try to gain insight into your main research question/s... I would say you are ready to go!
There are lots of tools out there to help users answer their biological questions. Nevertheless, users are ultimately responsible for understanding their datasets and make sure that use the tools they choose correctly. All program will (in general) generate an output file (or various output files) which users will need to understand to make sure that the results obtained are sensible according to the data they used, the filters they applied, the options they chose to run the program (reading documentation, while it may take a while, is key to properly use tools!). In case the output file/s display warnings/errors, users have to pay attention to what these warnings/errors mean: they can pinpoint issues with the input files, control files, options chosen, etc.; which are key to understand what may have gone wrong and what can be done to fix it.
Other people here may also want to add their own thoughts, which I am sure will complement what has already been discussed :)
Hope this helps!
S.