If your systems are load balanced, whether through hardware or software-based load balancing, you will achieve the best security coverage from Intruder by making sure that you've added all exposed systems as targets in the 'Targets' tab. This means adding every system which has at least one port/service exposed to the internet.
Typically, the underlying systems which the load-balancer sits in front of will not be exposed (they may be firewalled off from the internet, or sit on an internal network not accessible to Intruder's scanners). This means that Intruder will normally not be able to scan each individual server which the load balancer proxies traffic for.
If you're on the 'Pro' or 'Verified' plan, we recommend adding all of your targets to the platform as Smart Recon will tell you whether they are exposed or not. If they are, you can check Network View to see which ports and services in particular are open.