Hey, there. I’m currently a second year doctoral student and have been through the application process twice (once for this, once for my MA), so I thought I could offer you some general advice, with the caveat that, of course, all things vary by individual, by field, by program, etc.
My main piece of advice would be to take a lot of deep breaths and take your time. You say you’re not even sure what sort of program you want to do–this is something you need to be very certain about before you apply for anything. One of the worst things that could happen (and I’ve seen it happen for a lot of people) is that you apply to grad school directly after undergrad, plunge right into it and, six months or a year in, realize your program is a very bad fit for you, or that this sub-field isn’t at all what you really want to be studying. Graduate work requires such a level of dedication and personal involvement that it’s really, really miserable (and hard) to be doing your work on something you don’t 100% love. And, if you’re not truly “into” what you’re doing, a lot of times it shows, which makes your work look worse than that of students who have a genuine passion for their work, which won’t help you one bit in an enormously competitive field. To use a weddingbee-ish simile, it would be like getting married to the first person who sort of fit some critera you’d set out because you were worried you’d never get another chance! 🙂
So, honestly, take some time to really learn about your field and its different sub-fields and to research the different kinds of programs that are out there. Hold off applying for a year to do this if you have to (many, many people do). If you think that a year from now you’ll no longer feel like applying, then it’s probably not meant to be. If you have a real passion to go to graduate school and to make academia a full-time/life-long pursuit, it won’t make a difference if you’ve been out of school an extra six months or an extra ten years–you’ll still want to do it. And it might even help. I did a very half-ass application job to graduate school my senior year of undergrad because I didn’t know what else to do and I got rejected from everywhere I applied. I then got a job and worked for a few years (just a secretary job to pay the bills, not even anything in my field) and really became certain about what I genuinely wanted to do and when I applied again after that time it was with a real passion and determination (and also for a completely different field than the first time). I got accepted, got funding, and have been on this path ever since. I’m totally not unique. In my field, at least, I know hardly anyone who went straight from undergrad to graduate work. It’s very common and totally acceptable.
Regarding the rec letters: you don’t need to worry about it nearly as much as you are. If you have one really solid rec, from this professor you work with, that’s great. He/She really knows you and will likely write you something great. If the other two are still complimentary but less personal, then it’s not a big deal. It’s difficult to find opportunities for working intimately with professors as an undergrad and application committees understand this. Professors at your school also understand this and will, unless they’re really swamped with work or unless you had a bad relationship with them/turned in poor work, think nothing of writing you a perfectly nice rec letter. Even if they don’t remember you (like if it was a large lecture class, or a class you took with them several years earlier), they’ll usually just ask you to provide a paper or some exams you wrote for them and to see a CV or resume so that they can get a better idea of whether or not you have your head on straight, have a clear path to your academic goals, do good work, etc. It’s totally common.
And, if you do decide to put off applying until next year, that gives you a great opportunity to strengthen some of your professional relationships, get back in touch with professors, as them about the kind of work they do, about the field, etc. Do not hesitate to ask professors for advice, even former professors. Most will be happy to meet with you and talk about these things. They’re there because they have a passion for what they do and passionate people generally love talking about their passions.
One last thing–don’t underestimate the value of the GRE. Doing really well on it can help you jump through the first application round at a lot of programs and can also put you in line for better funding packages, awards, fellowships, etc. Definitely take some time to study for it and to learn the quirks of the exam itself. It’s a minor thing in the big picture, but it can really help you out at the start of your graduate career.
Sorry for the book! But I hope it’s helpful. Best of luck!