Wire Sponge Stage
When you come to a series of thin, vertical, flying platforms floating above a spike pit, jump onto the top of the first one. Then dash jump to the left, back to the wooden tree tunnel you just came through. Climb the wall to the first landing, and then dash jump off of it to the right, hit the steel wall, and climb up to the top of it. Once there, walk to the right and jump the gap; you'll run right into the Sub Tank.
Note it is possible, though not likely practical, to approach the Sub Tank from the right side next to the elevator shaft by exploiting the 'Neon Jump' trick (jump, air dash, then jump and release a second charge shot at the exact same time; the same frame), but this will require the Leg and Arm Upgrades.
Flame Stag Stage
At the beginning of the level find the first flying beetle. Jump on it's back and it will rise upwards. Let it rise as far as it will go. When you reach as far as it will go, you'll see a ledge on your left. Simply jump to it and find the Sub Tank.
If you accidentally destroy the flying beetle, it is possible to make it to the ledge with the Sub Tank by utilizing the charged Strike Chain or Speed Burner from the opposite ledge. This will obviously require the Arm Upgrade.
Magna Centipede Stage
Right before the first mini-boss room (Chop Register), there is a gap in the ceiling. If you are unsure of exactly where this is, utilize the Helmet Upgrade. Prior to reaching the gap, make sure when the six 'crusher' blocks fall to quickly pass over it when two have fallen by dash jumping. Immediately after a singular block will fall, ride it and quickly dash jump to the right and grip the wall to get the Sub Tank. Make sure the block is at its maximum horizontal distance right to make the jump, but do not wait to long; the block will fall down the pit. You only have one shot at it this way. Death or stage exit will be necessary if you fail.
Alternately, if you have the Arm Upgrade and the Speed Burner, you can just dash jump across the pit that precedes the gap in the ceiling, and at the height of your jump release a fully charged Speed Burner to dash into the wall that leads to the gap. This may take a few attempts; the Leg Upgrade's air dash prior to releasing the Speed Burner may help too.
Bubble Crab Stage
In the open water area, after the fish opens the big red door in the ground, there is a flat surface that stretches out for longer than most. the fish bot will glide very close to the ground here. Charge up Bubble Splash so you can jump super high. When you jump you'll see it on the left. When at the surface tap the jump key again to jump on the surface of the water and then jump to the left to collect the Sub Tank.
Alternatively, since X can jump higher when running down slopes, jump up while running down the small slope to the left of the flat surface to grip the lower wall to the left up in the air. This may take a few tries. Remember from the 'No Speed Burner' Centipede Heart Tank strategy that X can kick off really high walls more easily if you are not holding the directional buttons/analog stick in the direction of the wall you want to climb. Therefore, get close to the wall, stop your horizontal movement, then tap the jump button again to kick off the wall. Then wall jump up, spam the jump button to stay on the surface of the water under the alcove, move to the right to get out from under the alcove, and finally jump to your prize. This method cuts out having to revisit the stage. The jump can be made potentially easier by exploiting the 'Neon Jump' trick (jump, air dash, then jump and release a second charge shot at the exact same time; the same frame), but this will require the Leg and Arm Upgrades.