Dave
Generally speaking disabling aspects has a bad effect on the signal logic, for example disabling 'Approach Limited' will leave the logic with nothing to display when the next signal is showing 'Limited Clear' (red over flashing green), leaving the signal at danger as the only available alternative. The only time you should consider disabling aspects is when the list of available aspects in the signal mast table gets too long (CROR for example) when you manually control the aspects or only use LOGIXs to contol the signals, otherwise leave the logic to worry about what needs to be displayed.
The slow and limited indications should only show if there are track speed restrictions on the selected route, and this will typically happen by default when the selected route is going via the diverging route of a turnout. If you have a continuous run that makes for less than four signals in the circuit consider adding some intermediate virtual signals (with real detection blocks) so that the logic is able to work through more of the aspects.
I suspect that there is no simple answer to the SE8C flashing yellow conundrum. Setting the SE8C to do its own flashing yellow further restricts which aspects JMRI can display on the signal (no flashing red, flashing green or dark as well as no lunar) which would prevent many of the aspects from being displayed correctly.
Letting JMRI do the flashing should not be a huge problem on a small layout where in a worse case scenario only a quarter of the signal masts will display a flashing aspect, but if you have a lot of signals it would be better to use more modern signal mast decoders like the Signalist SC1 instead of the SE8C which support decoder controlled flashing on all of the aspects and just needs a single packet to set the whole mast when the aspect changes rather than the string of packets that the SE8C requires to set each head and further packets every time a lamp flashes.
Suzie x
Suzie Tall