There are a number of possibilities regarding the holes:
a) Have two layers of this pattern superimposed over one another.
b) Weave a single tire through what would become two holes as part of the weaving process. Once weaving is completed, insert extra tires internally through these, and then use tire strips to help hold in place.
c) Weave two tires through each hole perpendicular to each other.
d) After the base is created, add two perpendicular tires internally over each hole and connect them to the wall using tire strips.
e) After the base is created, weave lengths of tires slipped together like a long rope, in and out of adjacent holes in a line.
f) Push actual tires into the holes from the inside, possibly with tire or lashing through the tire middle to hold in place.
g) Use floatable styrene concrete blocks placed over the holes and strapped to the wall.
h) On the bottom section place large bags of gravel inside that would cover the holes, while providing ballast.
i) Leave the holes open at the bottom, but once it is in the water, and the plastic bottles float up with the tire section down, put extra plastic bottles through the holes to fill the bottom of the cavity. Attach cubes of gravel to the bottom, using the holes to secure with tire ropes, and then lashings to secure the cubes over the holes.
Just to consider the possibilities, I will show the first two in this list.