As I have no idea, if there is any tool to help you to place and connect parts on a matrix board, I'm went with what I used to.

Having the parts placed in my 3D CAD, I created a top an bottom view with the relevant parts:

I was planning to cut pieces from the trinket an the PiHat as both the corners are not carrying relevant traces (trinket just a mounting hole, easy to be sure, since layout is present/ PiHat datasheet of the DS3231 shows those pins are some of the many NC pins).

So I drew the matrix holes and the parts, using a color code to mark all pins connecting each other:

Pic is the one with the already placed parts with pins-to.connect close to each other.

Then place the connections with lines (of course the mechanical CAD does not prevent crossing "tracks". I finally found ways for all connections, shifting the RTC one row up, which spared me cutting something of the board. I used other line types for the respective "other side" of the board.

To not get lost in the process of placing parts and wires (tracks) in actual making, I doubles each view and deleted every part/wire I had placed in one view.