For those schools that we are eliminating, mostly due to not getting into the MT, is it better to withdrawal the application or decline? Or does it make no difference?
@soozievt will know the finer points of this, but as I understand you only “withdraw the application” if no decision has been made. Once the school offers admission (regardless of program) you need to decline the offer. If a form is provided, you can use that, or if there is an online portal or procedure, do that. Otherwise I think an email to the admissions department simply stating that you are declining the offer of admission at this time, is plenty.
At this point, once an admissions decision (acceptance) is made, then you would be declining the offer. It is nice to reply and decline. However, it is not imperative to do so, and it is assumed, if you do not put a deposit down by May 1. But you are not withdrawing an application once an admissions decision is reached, as @MTTwinsinCA correctly explained. 
If you decline as soon as you are certain (as opposed to taking no action & letting the offer expire 5/1), your spot may be more quickly opened up for a WL student.
We had my S narrow down his acceptances and wait lists last weekend. There are a lot of kids on wait lists or who haven’t heard from schools who have kids on holds so we wanted to make sure those kids had the opportunity for those spots. We sent declines of acceptances and removal from wait list responses by returning the No I’m not attending reply cards or e-mails to the undergraduate admissions department if there was no reply card. For a couple of them, we also separately emailed the Musical Theatre department contact person via email so they were aware and could more quickly offer someone else the spots if applicable.