Hi,
You have to decide first what you want. A general simple way to send mails (using javamail/smtp) or a more complex, more powerful Lotus Domino way using the mentioned toolkit. Do you also want to read mails or manipulate mails in an mailbox?
It is not very difficult to send mails using smtp and the javamail API, in another
thread I found
this link with some explanation. This option has (almost) nothing to do with Lotus Domino at all, the only thing you need is an smtp server, but this is for the system admin to setup and configure, you only need an ip-address/port (and maybe username/password). (Another way is looking at Apache Commons Mail, which even simplifies working with the javamail API).
Working "the Domino way" gives you a lot of power (programmatically moves mails to different folders, adding properties to mails...) but is a lot more difficult to do. This has nothing to do anymore with the javamail API, but all with the toolkit.
I guess you want the first thing. In that case, read up on the javamail api and talk to your system admin about smtp. Sending a mail will only be a few lines of code in that case.