Yes, the Map to Reference assembler can handle multiple reference sequences. Your reference sequences can either:
1. be grouped into a sequence list (Do this using Sequence→Group Sequences into a List...) and then select this list for the reference, or
2. You can use the "choose" button within Map to Reference settings and select any number of reference sequences within your database.
Geneious will then try all reads against all references in a single operation.
If you want to map all reads to each reference sequence in separate assemblies, use the Workflow "Map reads to each reference sequence". This is available under Tools > Workflows.
If you have Sanger reads representing several different clones that need to be mapped to their respective reference, try the Cloning Validation tool, which can visually group your reads into clones, map those clones to your reference(s), and automate validation of your sequences so that you can quickly move from sequences to results.
If you have a lot of shorter reference sequences, consider combining them using the concatenation tool into a single sequence with N spacers between each sequence. This will prevent a situation you can get where you run out of open file handles and you’ll also just get a single contig document produced rather than many (See this article for more information)