The Gibson Assembly tool in Geneious Prime can be used to create new vectors with swapped parts while simultaneously generating the necessary overlapping primers. For example, Gibson Assembly can be used if you need to swap components (e.g. election markers) between two plasmids that are missing convenient restriction enzyme sites. The schematic below demonstrates how this would be achieved and we can simulate the reaction in Geneious Prime.
To do this, first select the component that will be transferred from your donor plasmid and use Extract to create a new sequence document containing only the region of interest. No PCR primers need to be made for our purposes, but you could extract by PCR to create this product. Next, select the recipient plasmid by first selecting the piece to be replaced, and then right-click and select inverse selection. With the selection made, create a set of precise primers and extract a PCR product.
Next, simply select your two fragments and start the Gibson Assembly tool. The larger fragment should automatically be chosen as the backbone, but this can be rearranged by either dragging the components into the correct order, or selecting the appropriate component from the backbone dropdown menu. Choose "save unique primers"(to save your overlap primers necessary for generating a PCR product with homologous ends) and click "Generate Constructs" to complete the assembly.