I have an entry level Nikon (3300) with the standard lens, I know its not the best setup but I'd like to get the most out of it, what's the best way to break into manual mode and start understanding how best to use it ?
Not sure what point you're starting from - so the most basic starting point is learn what Aperture, Exposure, and ISO are. For a 20 second run down:
Aperture is the name of the variable sized hole inside the lens. This can be used to control how much light reaches the sensor, and also how much "depth-of-field" ("DOF") you get, which refers to how much of the scene is in focus - ie: just a sliver, or everything in sight. Smaller f/ number means more light in, less DOF. Bigger DOF means less light in, but deeper DOF.
Exposure (time) is how long you leave the sensor exposed to the light. More time makes the photo brighter, less time darker.
ISO is a reference to how film sensitivities were measured, but is still basically true for digital. The lower the number, the less sensitive to light the sensor is, high the number the more sensitive.
Learning how these can be balanced in a practical sense is really key to anything other than Auto mode.
For getting away from Auto mode - I'm a big fan of Aperture Priority mode. This mode means you set an Aperture and ISO, and the camera decides the Exposure time. This gets you thinking about what aperture you want (ie: small f/ number for narrow DOF portraits, or mid to small f/ number for landscapes). It is worth going out specifically to take photos while you're adjusting to this mode though, as being honest you/I/whoever is probably going to balls
a lot of them up while getting adjusted to things. This is because you still need to be somewhat mindful of keeping an eye on ISO setting and camera-selected Exposure times. For example, if shooting deep DOF landscapes, with low ISO - the camera's going to set itself a long Exposure time. That's fine if you're working on a tripod to keep the camera stable, but not great if you're trying to shoot a 5 second exposures hand held, or try and take a quick snap of the missus, kid, pet dog, whatever while forgetting you've left it on Aperture Priority and end up with a 15 second impromptu "modern artwork". Basically just experiment a lot, keep an eye on roughly what shutter speeds (Exposure) the camera is setting, and you'll get a feel for what you can shoot hand held, and what you need a tripod for. Then you start to get a feel for when you need to raise ISO to keep Exposure hand-holdable, or to sacrifice a little DOF and open the aperture up to let more light in. If you shoot around sunset and roll through dusk, you'll realise just how quickly exposure requirements can change, and how quickly you can end up needing a tripod. If you do get or have a tripod, longer exposures can be your friend if you like the smooth water style photos, or light-trails. But work on the basics, be prepared to stuff up a lot, and keep on trying until you get your head around it.
One thing no-one told me until quite a while into when I had been shooting, was about "stops". The name itself is irrelevant, but what it refers to is the "square rule" of light, which basically refers to exposures following an exponential curve. For each time you want to double the brightness of your image, you have to double either the exposure time or ISO sensitivity, or open your Aperture a "full stop". Most modern cameras have all the 'exposure triangle' settings (Aperture, Exposure and ISO) divided into third-"stops". What I didn't know until later, was that meant if shooting manual - if you already have a perfectly exposed shot - but want to make the Exposure time longer for example, for each adjustment 'click' to Exposure, you need to balance it by either going one 'click' less sensitive on ISO or closing the aperture one 'click'. So if you want 5sec @ f/4.0, ISO200 to become a 10sec exposure (3-clicks from 5sec generally being 6sec, 8sec, 10sec) - you could use either 10sec @ f/5.6, ISO200, (3-clicks from f/4 through f/4.5, f/5, f/5.6) or 10sec @ f/4.0 ISO100 (3-clicks from ISO200, through ISO160, ISO125, ISO100).
While this quite possibly all sounds massively complex and difficult - once you work out what they actually do in a real world sense, and tinker round with it a bit - it's fairly straight forward.
Some random examples from my archives:
Shallow DOF:
Small Scale
Borage Flower
Deep DOF:
Tasmania, 2018
Anchored
Long Exposure:
Portsea Piers
Long Exposure (with star trails):
Celestial Canopy
Hopefully that's some use anyway and not overly-confusing. If there's anything in particular you're struggling with, let me know.