The option disappeared in Orbeon Forms 4.0, as we thought this would be better done as a global or a per-app setting. However that setting hasn't been implemented yet.
So at this point there is no direct way to pick a logo via Form Builder.
This custom CSS can be used to hide the Orbeon logo:
.navbar .container img {
display: none;
}
You should be able to add your own logo with CSS along the lines of:
.navbar .container {
background-image: url(my-logo.png)
}
Some other CSS tweaks might be needed, but it's doable.
UPDATE:
I forgot about this property, which you can override:
<property
as="xs:anyURI"
name="oxf.fr.default-logo.uri.*.*"
value="/apps/fr/style/orbeon-navbar-logo.png"/>