F2, 1, 2, 1+2 builds the most meter. I usually use it after a blocked jump-in punch. The jip, F2, 1 can be hit confirmed into a Red Dash, Down Slash but can be difficult to do.
1, 1, 4 staggers the opponent on hit so you can Red Dash and start 1, 1, 4 again or finish with Red Slide. If it hits an aerial opponent you can hit confirm it into Red Dash Up Slash. I usually use 1, 1, 4 after a standing reset (1, 1, 2) because you can confirm it into EX Dagger if your opponent is stand blocking.
1, 1, 2 I only use at the end of every combo because it disables wake-ups and gives you mix-ups.
F4, 3 I use it as an anti-air because it's safe and has two hits. You can hit confirm the F4 into Red Dash, Up/Down Slash. I also use it when I have my opponent in the corner.
B1, 1, F4 is used if my opponent is a low hitbox character. All of Skarlet's other fast strings whiff on crouch on characters like Mileena. I use this string after a blocked EX Dagger when my opponent is crouch blocking (usually happens at the end of a combo 1, 1, 2, EX Dagger). B1, 1, 4 is also used in Skarlet's wall combos. You can see her combos in Ninj's combo guide. If you're close to the corner, you can do B1, 1, F4, Red Dash, Down Slash to get the opponent in the corner.
U3 is used as a blocked teleport punisher. U3, U3, Air Dagger, dash, 2 or 3, Dagger Toss (dash cancel), 1, 1, 2. There is a stronger varient of this combo but it is harder to do. Check Ninj's combo guide.
F4, Red Dash or D4, Red Dash are her best for footsies because of their range and cancel advantage.
It is important to use a Red Dash after all of her blockstrings so you can start mix-ups. You should also note which strings can jail the opponent standing so you can use an EX Dagger and dash cancel into another blockstring. F2, 1, 2, 1+2 / 1, 1, 4 / 1, 1, 2 all jail the opponent standing. There are a few others but those are the ones you really need.
I personally don't bother with her other strings like F3, 1, 2 or F3, 3 since they are either too slow and/or punishable on block. Once people start learning how to fight Skarlet, these strings will be beaten out every time. This is just my opinion though.