Read files from paired-end sequencing need to be paired in Geneious before the pairing information can be used in assembly. This can be done using the Set Paired Reads option under the Sequence menu. For example if you have two FASTQ files, one with forward reads and one with reverse reads, you should select both, go to Set Paired Reads, and choose the appropriate settings such as the expected distance between pairs. This will generate a new paired reads file containing the linked reads.
Note that the paired distance you set does not need to be exact for all reads. If you have a range of insert sizes, you should set it on the mid point of the range. Geneious will still assemble reads that are under or over the expected distance, but the pairing information will be used to help the assembler resolve complex placement issues.
From R11 onwards, you will be prompted to set paired reads during the file import process if Geneious detects that your fastq files are likely to contain paired reads.