I've usually done as follows;
-Attach any needed spacers to the first baffle using masking tape (2x4 scraps work great) so that when I stick the baffle into place the spacer will butt up against the end of the tank and keep it aligned corrrectly until the silicone sets
-Run a bead of silicone right where I want to place that first baffle
-Starting in the middle of the tank, and working toward the ends, slide the baffle into the silicone bead. The baffle will push some of the silicone ahead of itself so that you end up with a bead of silicone in front of the baffle, and a thin bead between the baffel and the tank wall.
-Run a similar bead of silicone on the other side of the baffle so that the baffle has a bead in front and in back. (If you can reach them, smooth the beads out with a gloved finger, plastic spoon, ice cube, corner of a credit card or whatever else might be handy.)
-Once the first baffle is in place, basically repeat the same process with the additional baffles working out from the end of the tank toward the middle. I try to do it so that the first baffle (closest to the end of the tank) is braced to the end of the tank with a spacer, and then the rest are sandwiched against it with additional spacers kind of like the alternating bread and meat on a big mac. Just be careful to chose spacers that you will be able to get out - obviously...
To avoid a big mess, have a trash container handy and easily accessibly, a bunch of paper towells, and several pairs of rubber gloves. Change the gloves as soon as they get silicone on them, otherwise it will be everywhere.
Using masking tape to edge the seams makes everything come out looking really clean. Remove the tape as soon as the seams are smoothed out. If you can't reach some of the seams to smooth them out, it's probably best to not try so you don't end up with a big smear.
HTH