There is a new view for "Matters Eligible for Retainer" that will help you apply retainers to matters easily. This is a better approach where you can see and select the matters to apply retainers to more specifically instead of the previous more blind "Apply All Retainers". 

Also, applying retainers can be done at any time during the month and will be applied to any Invoice that has been approved.

Finally, simplifying how things are handled with the disbursement and allocations has allowed us to keep the invoice clean with a single payment shown to your client.

See this user guide here for more details.