The best way to do it is to have them change the filter (if you indeed to have a filter, some trans's only have a metal screen for the large bits) and then do a flush.
A lot of shops when it's a flush, only do a flush, they don't change the filter. Flush's at a stealership should be around $100-$130, with a filter change anywhere from $160-$180.
The most important thing to make sure of is you ensure, prior to letting them do this, that they use the correct fluid when doing the flush; and even stealerships do not use the correct fluid, or even their brands OEM fluid. If for example your trans is spec'd for Mercon V, you don't let them use Mercon and then an additive to "bring it up" to Mercon V spec - this is BS and the cheap way out for them.
Also, you do not need trans flush additive or after flush additive installed. You only should be having straight trans fluid, of the correct certified type, run through the trans, that's it.
Excuses like, 'That's what we've always used', and, 'We've never had a problem', are not acceptable. Wear, that they nor you would ever be able to measure, from improper frictional characteristics from using the wrong fluid, or seal damage from using a harsh flush additive, will not manifest itself (unless it's an extreme example) for many thousands of miles. What would they say if you brought it in and had problems at that point? 'Oh, couldn't have been our stuff, must be something else...'
It's your $$$, both for the flush and for your trans when it dies because they decided on your behalf to take the cheap way out...make sure you check and insist on this stuff upfront.
Chuck