Bubbles work pretty much how projectiles work in SF, they eat up a portion of the screen. Algol can have 4 bubbles at once on the screen at a time, and can change patterns with them, etc. When he shoots a fifth bubble, the oldest bubble disappears.
Each bubble has a different use but until Algol gets at least two or more bubbles on screen it's REALLY risky for him to shoot bubbles (charged bubbles carry greater risk in this instance) versus several characters. It's low reward/high risk to shoot any charged bubble versus, say Nightmare, who can trade 33B with the bubble from just about anywhere, launch you, and then continue on to get a very large combo + tech trap that ends up taking about half life.
On the flip side, bubbles almost completely nullify a few characters, like Taki/Talim/Yoda, who have almost nothing they can do about bubble shields. (All are short range characters that, Talim moreso then Taki, require using Jumping-based moves to get in, which means they are very easy to start bubble combos on from random bubbles) In this case spamming bubbles becomes low risk/high reward.
Bubbles allow Algol to use his otherwise fairly terrible long range pokes safely.
You probably already have a feel for what to do with what bubbles, it's pretty obvious with a little practice-
6A+B_[A+B] - Zoneing, covers the whole stage, loses to GI/certain tech crouching moves/any step
2A+B_[A+B] - Zoneing, covers only a small portion in front of Algol, loses to GI/any step, but depending upon when it's GI'd it may or may not hit Algol
4A+B - mid_long range step shield.
4[A+B]- Full body shield, little range/movement but protects front and then eventually Algol's sides.
FC A+B- Crouching bubble, works like 6A+B but kills TC moves.
22_88A+B- Retreating bubbles, weird/terribile hitboxes but pretty much safe v. GI. Last resort escape, poor recovery.
Probably the most common pattern is:
4[A+B], 2A+B- shields immediate stepping around and in front of him, then the 2A+B intercepts low pokes that go under bubbles. 4A+B in itself is pretty risky if the enemy can see it on reaction- the bubbles itself come out fast but add the time it takes for the 4A+B to come out PLUS the recovery Algol goes through if bubbles aren't blocked at point blank range, A simple GI means you can end up eating your own bubbles for free regardless of where you are. I have to be very careful with when and where I use 4[A+B] here (and will sometimes go for 4A+B instead, which is better for hitting steppers/8WRs at mid/long range) because we do have local players that look for the white flash then run up and GI me.