What to do if you find yourself stuck with no hope of rescue: Consider yourself lucky that life has been good to you so far. Alternatively, if life hasn't been good to you so far—which, given your present circumstances, seems more likely—consider yourself lucky that it won't be troubling you much longer. -Hitchiker's Guide to the Galaxy
Sometimes the answer to this sort of thing is "everybody dies." In fact, that's usually how it goes with major mishaps. The real question is how well you prepared for the unknown unknowns. Rumsfeld got laughed at for that phrase, "the unknown unknowns," but it really is the key. How do you deal with the things you don't know about until you know about them.
Hopefully your ship has a large amount of rations. You may need months of rations to pull this off. Living on a foreign environment is extremely tough. You're going to need to be almost completely reliant on rations in the beginning, and hopefully be able to ween yourself off of them as time progresses.
In survival situations there's an order of operations that is universally recommended: Air, shelter, water, food. It's known as the rule of 3's based on how long you can last without them: the human body can survive 3 minutes without air, 3 hours without shelter (in a harsh environment), 3 days without water, and 3 weeks without food. You say it's a habitable planet, so let's assume that air is easy, and you say you have an abandoned ship to work with, so you probably have shelter. So let's get to work on the others.
The first step would be water. Hopefully you have a reasonable supply of water on board, but it might damaged. Setting up survival tools like solar stills may be essential. They have the advantage of also purifying the water before you drink it, which has benefits in an alien landscape. However, you weren't too interested in water, you were interested in food. That puts us in the weeks timeframe, plus whatever rations you have.
Now the good news is that it is highly unlikely that anything in this ecosystem is going to be gratuitously toxic. Most toxins are co-evolved with the particular life they grow up around. For example, lactotoxin, the toxin in Black Widow venom, specifically targets neurons, binding to protein structures that identify them. You are an alien in this environment, so are likely to not be targeted by their targeted toxins. You're more likely going to have to deal with very simplistic chemical attacks (acid/base, redox) and accidental toxicities (like heavy metals).
The good news is that our bodies are designed to deal with this sort of thing. In survival they teach you an approach to minimize the risk of poisoning yourself with an unknown food source. The first step is not to eat unknown things, though survival situations rarely let you be so picky. If you do need to eat something unknown, you do it in stages. First you rub a bit of it on your skin. Our skin is an amazing rejecter of a lot of bad things, and it tends to respond to attacks. You look for redness. If you swell up here, be glad you didn't eat the food first. After an hour/few hours, you can try rubbing it on your lips. Lips are a lot thinner and more sensitive. One of their evolutionary jobs is to detect the difference between food and not food, so they're good at it. If you have no reaction, you use your tongue. Then you finally take a nibble. Each time, you give your body (the world's most advanced chemistry set) time to analyze the compounds.
That should pick up all basic acute toxicity issues, and because you're the alien, you're unlikely to have to deal with any subtle toxicities. So that answers the first half: how to determine it's not poisonous.
The latter half is trickier. There's a really good chance that the ecosystem you landed on doesn't support the amino acids we need. We're going to have to be creative.
The first step for food is sugars. Your body needs something to burn. That's the first layer of nutrition. It can burn a lot of things, like fatty acids, so if you find those, great. However, you're most likely to find sugars because they're simple. They're also pretty easy to find because, evolutionarily, we needed to find them. Our tongue is remarkably good at determining what has sugar content in it.
The next layer is minerals. These may be harder to get from the edible foods around you because they will have arrived at a different balance of minerals than we need. We actually don't need much (most primitive cultures ate several hundred times the US RDA of many minerals that we have trouble finding in our diet today!), but if we did have trouble, I'd go straight to the source: dirt. There are famous clay licks for parrots who live in environments which are short on minerals. Clays are an amazingly good source of them. You might find that mud pie is actually on the menu.
The hardest part would be the amino acids. Nine of them are simply required by the human body: phenylalanine, valine, threonine, tryptophan, methionine, leucine, isoleucine, lysine, and histidine. Five more are considered important because we only create them within our body in times of great stress: arginine, cysteine, glycine, glutamine, proline, and tyrosine. Finding these could be very difficult. It's highly unlikely that the life on this other planet has these amino acids. You're going to have to be creative.
Or you need to enlist creativity. Consider yeast. Yeast is known to produce many of the essential amino acids we need. And, unlike you're crew, you're comfortable if a few billion of them die trying to evolve to adapt to the environment you're in. Yeast is your single-celled weapon of choice in this foreign environment. It will naturally breed within the human-controlled areas, but may also be in the best position possible to evolve into something that can function in the alien ecosystem. Careful cultivation of yeasts to survive the harsh climate may be your best bet for generating the very exacting amino acids you need to survive.
Beyond that, it's all really guesswork. I'd say your success is based 0.00001% on how prepared your crew is to survive, and 99.99999% based on the particular chemistries of the planet you landed on. To make your story more believable, I'd recommend choosing a few atypical chemistries to apply to your planet which your crew can then find clever ways to take advantage of to make it feel more realistic. You're not trying to make the planet into your home, you're trying to survive on the planet you've been given.
