My character is basically trying to help all of the factions, especially the NCR, even if in the end she'll most probably choose the "Wild Card" ending. I'm doing this because trying to be on the good side of as many factions as possible allows me to enjoy more of the plot and discover the story behind each one of them.
I already had to become enemy with the Powder Gangers (well, can't please everyone), but now I wonder: can I try to help the Legion for as much as possible, before turning against them? Is it possible to advance the plotlines of all the main factions until a rather advanced point, where I'll have to make my final choice?

To a point yes...
You can help CL go against House, you can help the bad strip families instead of hurt their neferious parades schemes.
You don't have to go to the dam, you can just let the President die without any effort at all.
With thought you can help / hurt / ignore all of them as much as you like..

However walruss, it comes to naught, zero, zilch, 9.. it's fun to do so, but the ending is no different from a normal House / Yesbot run.

Not really worth it, since the only interesting Legion quest involves killing NCR officers.

Is that so? I wanted to keep the Legion friendly for a while, in order to know more about them. I don't like the Omertas or the White Glove Society either, but I did their questlines in order to know their story.

However, if helping the Legion doesn't bring many interesting plotlines, then it doesn't matter for me to keep them friendly... but I did hear something about Vulpes being killed by the Legion for some reason? I'd like to see that scene.

At some point you'll get a quest that informs you that doing more missions for one faction will garner you distrust from others. If you continue those quest paths will be closed.
Also helping the Legion will not work out very well for you in certain quests (Omertas, White Glove Society), with regards to a non-Legion ending slides.

Ah, so there's a warning when it's time to choose a definitive faction? I want to follow the Yes Man path, but I worry that my trend of trying to keep all factions friendly may mess it up.

Nothing will or can mess up that ending, unless a bug pops up.
Really have fun plotting out how to keep them all happy, as it is fun to do so.

Yesbots quests are open to anything and everything up to a point, really it can be molded however you like..
Apart from the finale and the epilogue credits.

To check if you've PO a faction, you need to keep an eye out on these two quests..
Don't tred on the bear.. NCR if you follow yes man this should only fail at the end quests proper.
Beware the wrath of caesar.. CL this is the tricky one to avoid this you need to help the evil strip factions, even then later on it will fail.
Though you get to see how far it takes to do so.

And is there a way to not get Benny killed while still remaining friendly with the Legion? If I don't choose to talk with Benny and just leave him there, will he just remain there tied up until when I've decided to go against the Legion and free him?

I have no clue Benny wise, I'm sorry to say, I tend to kill him on sight.
Maybe if you stealth kill all the guards / no named NPC's, release benny and run for it..
Wait a few days in an indoors location to check if they'll reset.
If however you fail the Beware the wrath of caesar quest doing this I would say no there is no way.

I've done this myself, it is fun trying to get along with everyone for whatever reasons, roleplaying undercover until I decided what was best was mine. At the moment I'm liked with everyone except PG's and I've done no evil quests except for killing Mr House, on a side note I made Caesar froth at the mouth with some of the things I'd done which in itself was fun. I've got all the safehouses at the moment and I am in no hurry to advance the plot, so I'm staying away from the major quests. With Benny as soon as you help him in any way you trigger Legion quest failures and there's no going back. (thats what happened to me anyway when I tried it)

The downside of this undercover stuff for me is I wish there were some way of telling Boone I don't really work for the Legion.

I get all the Safehouses from each faction and then decide what to do next.


B)

So it looks like saving Benny will inevitably trigger Legion hostility. I could just kill him and be done with it, but... so far I'm roleplay the game just as I want so I have this pet peeve to do everything -exactly- as I please.

Here's a question then: can I just let Benny tied up in Caesar's tent while I proceed doing Legion quests? So I can advance Legion questlines as long as I want, until I decide to end the Legion path by freeing Benny?

Do you have the poker chip, or will Caesar give it too you.
If so than maybe you could just do the legion quests.
However that all depends on caesar, if the only dialogue he brings up is about killing Benny than you've got your answer.
If he talks about the bunker under the hill or how you can help him then it'll still be impossible.