Been a while since I wrote one of these.
JKS have been causing people a few headaches so I thought I would write a guide on this
A) Talk about JKS, keytool and KeyStore Explorer
B) Create a JKS - letsencrypt.jks with a RSA 2048 key (simple-cert)
C) Add a second RSA 4096 key - (san-cert)
D) Create a CSR for simple-cert and a CSR for san-cert
E) Complete Challenges with Certbot
F) Add certificates to KeyStore and Verify
G) Add To Tomacat 8.x and Verifying Certificate and JKS Functioning
H) Converting Standard certbot artifacts to a JKS (thanks to @sahsanu)
I) Creating JKS files with Bash and OpenSSL
J) Using pyjks for creating JKS files with Hooks
K) Dealing with Intermediates and Roots - options and ground work
Hope this helps out and clarifies some things out.