i see that there is an option an SSL / Business License Installation but is it possible to use my own ssl cert?
No, currently Tonido can only use our generated SSL certificates.
Second, the plan being to use my own domain name with dyndns. Would that work too or no?
Yes that would work fine. You can use your own domain.
If you are going to use our relay service then you can use only our own domain. If you are portforwarding then you can use whichever domain you want.