You can't target an engulfed creature (nor affect it with areas).
Targeting a creature with effects, of affecting it with areas, requires line of effect:
When creating an effect, you usually need an unblocked path to the target of a spell, the origin point of an effect’s area, or the place where you create something with a spell or other ability. This is called a line of effect. You have line of effect unless a creature is entirely behind a solid physical barrier. Visibility doesn’t matter for line of effect, nor do portcullises and other barriers that aren’t totally solid. If you’re unsure whether a barrier is solid enough, usually a 1-foot-square gap is enough to maintain a line of effect, though the GM makes the final call.
In an area effect, creatures or targets must have line of effect to the point of origin to be affected. If there’s no line of effect between the origin of the area and the target, the effect doesn’t apply to that target. For example, if there’s a solid wall between the origin of a fireball and a creature that’s within the burst radius, the wall blocks the effect—that creature is unaffected by the fireball and doesn’t need to attempt a save against it. Likewise, any ongoing effects created by an ability with an area cease to affect anyone who moves outside of the line of effect.
Emphasis mine. As you can see, visibility doesn't matter, so the engulfing creature being transparent wouldn't allow you to target the engulfed creature, the usual exception would be visual effects, like the gaze special ability some creatures have.
You can use some of this to your benefit though, since you have no risk of accidentally affecting engulfed creatures, you can use area effects against the engulfing creature without worrying about your engulfed ally being affected.