here is a common set of best practices for 9800 controllers, but keep in mind that some best practices may not be the best practices for your environment. So read the features carefully, cross check against the site survey's you may have performed and the design requirements then deploy it.
https://www.cisco.com/c/en/us/products/collateral/wireless/catalyst-9800-series-wireless-controllers/guide-c07-743627.html
Below are the best practices to deploy 9800-CL in Hypervisors.
https://www.cisco.com/c/en/us/products/collateral/wireless/catalyst-9800-cl-wireless-controller-cloud/nb-06-cat9800-cl-wirel-cloud-dep-guide-cte-en.html
Regarding the migration make sure that;
1. Upgrade your existing 5508 to IRCM capable TAC recommended image and build the mobility tunnels. Recommended images are https://www.cisco.com/c/en/us/support/docs/wireless/wireless-lan-controller-software/200046-tac-recommended-aireos.html
2. you migrate one single roaming domain at a time (roaming domain can be one floor or building where an user roams without any signal blackspots) , do not have AP's in certain floor registered to different controllers.
3. Do not do salt and pepper deployments (Mix and match different generations of AP's in one single roaming domain)
4. Check the existing AP model compatibility with 9800 (X600 series AP's are not supported and Wave 1 AP's are last supported in 17.3.x).
5. Use TAC recommended codes in new 9800.
https://www.cisco.com/c/en/us/support/docs/wireless/catalyst-9800-series-wireless-controllers/214749-tac-recommended-ios-xe-builds-for-wirele.html
