Kleiner Perkins Caufield & Byers partner Aileen Lee is starting a new seed fund that will be affiliated with — but separate from — KP, according to an interview this morning with Lee and Kleiner’s John Doerr.

The not-quite-yet launched fund doesn’t have a name, and Lee can’t talk about how much she’s raising, since it’s still in process. My guess is it’s likely to be in the $50 million range. Another guess is that she won’t have a hard time raising the money, despite a glut of seed funds that have had a challenging time positioning themselves in the market after the great seed fund boom of 2010. Said Doerr, “Very few people know what she’s doing, but they’re beating down the doors.”

Aileen Lee joined KP in 1999, and she has long been more about working hard with entrepreneurs than making a big brand for herself. In recent years, her profile has risen with some excellent guest posts on tech blogs and investments in the commerce space like Rent the Runway and One Kings Lane.

The move came more out of Lee’s passion for working with very early stage companies than any strategic move on Kleiner’s part. “I think it’s a really important part of the life-cycle of these companies, more so than ever before,” she said. “I like to be part of the trusted pit crew they are looking to for guidance. I look at the companies I am working with now, and I wish that I’d been all of their seed investor.”

Lee says she’ll differentiate the firm by offering hands-on help well after the initial investment. That sounds like something everyone does — because everyone says they do it — but a lot don’t. In fact, a lot of angels believe that entrepreneurs mostly want to be left alone.

That’s clearly not Lee’s ethos. Kleiner, too, has long been known as a firm that offers a lot of hands-on help with companies, particularly with building out management teams. This fund is clearly coming out of that cultural tradition. “I think Aileen’s approach is not trying to spray and pray, but rather to find entrepreneurs who want to plant a seed with us and be more selective,” Doerr said. That is different than many seed funds.

The messaging on the relationship between the two firms is a little tricky. Doerr emphasized that Lee was still very much a partner in existing Kleiner funds and fulfilling her board obligations to her companies — which are some of the hottest in the firm’s portfolio. But part of the reason Kleiner was interested in the partnership is that Lee’s fund would be a separate entity not under Kleiner’s authority.

At the same time, Kleiner will continue to make its own seed investments, but it’s clearly not the firm’s focus. Doerr said that knowing a longtime trusted partner would be spending all of her time digging in that ecosystem would be a big plus for Kleiner.

It’ll be a fine line to walk for Lee: To get out of the shadow of the grand Kleiner name while at the same time, using the advantage of that link. Some entrepreneurs will value the autonomy, and others will value the affiliation.

With lower capitalization rates, the seed-stage has become a crucial place for investors to gain a foothold in young companies. The top firms have all struggled to find the right method to get in the mix. Doerr says his partnership has had long meetings about what it should do or not do when it comes to seed investing, and there’s no easy consensus. The firm has done these days since 1972, when it invested $100,000 in Genentech in $10,000 increments. That yielded an $80 billion company, not to mention the dawning of a new age of biotechnology.

But a pure focus on seed investing clearly has its advantages, and big venture firms all want to find a way to get some of that. For Kleiner, it’ll be Lee’s affiliated fund that has its own autonomy — in case entrepreneurs just don’t want a big fund in that earliest round. Greylock, and many others, have gone the route of a special “Discovery Fund,” for smaller investments. Andreessen Horowitz has more of a grab bag approach, doing everything from a tiny seed deal to a Skype buyout out of one fund, while allowing general partners to make their own angel investments on the side as well.

The latter is the diciest question for firms these days: Whether partners should be allowed to angel invest on the side. It’s particularly of note since Jim Breyer made a killing with his personal investment in Facebook alongside of Accel’s. But should he have? Or should all of the stake have gone to Accel’s LPs?

Some firms, like Kleiner, believe it’s a conflict of interest for partners to angel invest. Others believe that entrepreneurs will only do those early deals with individuals, and that it’s better to be involved than not. The biggest example of that may be Roger McNamee’s angel investment in Facebook, which cemented a relationship that allowed Elevation to invest in the company more heavily just before its valuation went to the moon. That bet essentially saved Elevation’s first fund. Still more firms get around this by asking one-off permission to angel invest or requiring that partners donate the upside of a personal deal to the fund. Benchmark, for instance, does the latter.

I got a Master class in all the differences, during Pando’s fundraising, an inside look at how much each partnership is grappling with this. (While we’re disclosing things, Marc Andreessen, Accel, Greylock, and Matt Cohler of Benchmark are all investors in Pando. No one from Kleiner is. For the full list go here.)

We look forward to seeing how Lee continues to differentiate herself from the landscape. We will report more details on the firm’s name, size, and first few deals as soon as we hear about them.