Creating multi-gene phylogenetic trees involves aligning individual genes from each taxon, followed by concatenation of alignments, and finally tree building. Here's how to perform each step in Geneious Prime:
You may already have gene sequences separated or extracted and can skip some of the steps here.
In this example, I'll start by extracting annotations from whole bacterial genomes. I have a list of gene annotations that I know exist in all of my taxa, so I'm simply filtering the annotations for those using an OR statement and clicking "extract".
In order to make sorting of the genes easier, rename the extracted sequences so that they start with their gene name, followed by the source sequence name. To do so, use Edit -> Batch Rename and set it to rename "Sequences in Sequence List" -> Property "Name of Sequence" and using the advanced options, replace the entire field with the added property from annotation names and sequence name as demonstrated below.
Next, group the sequences by gene name using a workflow: "Group Sequences by Name" (I'm using underscore "_" as the separator, which I created in the last step).
Now align each separately with another workflow: "Batch Align with MAFFT".
Note that you can perform the same workflow with any of the MSA algorithms if needed.
Finally, concatenate the alignments (by index) and you're ready to build your tree with any of the available tree builders.