What is the best way to break up scans so they don't use licenses up and so scans don't end up getting blocked?

I would recommend to break in to groups based on your organization and run host discovery first and run asset based scanning to avoid this situation. e.g. - if you company has two offices one is US and other in UK and each location has about 15 V-LANs, that also u brake in to Server, Network and PC (remember always keep your V-LANs segregated) this way it will be easy to manage vulnerabilities and easy for reporting as well. so based on this segregation you run the split the host discovery also which will be faster than running all the V-LANs host discovery. Then create assets based on ur preference (DNS, IP, etc..) then run full scan on them to avoid licensing issues. Also if you have Nessus manager and if your not fully utilizing the license use them on the servers.