Is the ADC output a fixed-point format, or it shouldn't be considered as any format?
Without a format, the ADC output would be meaningless ones and zeros (or voltage levels, because mapping from a voltage to a 1 or a 0 is part of the format).
So -- yes, there's a format there. It's probably simple unsigned binary, but part of the format that you need to know is where the MSB, LSB, and all the significant bits in between are.
What does the output of my filter represent?
That depends on your system. You know what's feeding the ADC -- you should be able to figure out (or ask) what the voltage applied to the ADC means. From that you can figure out what the number out of the ADC means. From that, and the nature of the filter, then you can figure out what the number out of the filter means.
For instance, if the voltage going into the ADC came from a water level meter of some pond that's open to the air, then you'd expect a signal that averages out to the actual liquid level in the pond, but that would have some chop on windy days. From that, you could deduce that perhaps you need a low-pass filter to get just the average liquid level while ignoring the chop -- and you could figure out the correct scaling for your filter output to get the pond level into feet or meters or cubits or whatever.
If some of the coefficients are negative, what does a negative output mean?
First, you can have negative coefficients and a filter that's well-damped enough that for non-negative inputs the output never goes negative.
Second, there's a lot of reasons a filter output may go negative, so "what does it mean?" is vague. If it's supposed to be a low-pass filter, it means you have some overshoot, but what it means is a system-level question that you need to answer. On the other hand, if it's a high-pass filter then of course the output will go negative, because a high-pass filter, by definition, has a zero average so any positive excursion demands a negative excursion to even things out.
If the coefficients are represented in Q6.10 format for example, does the output need to be shifted?
Again, this is a system question, and it really has more to do with the filter's transfer function and what the desired output of the filter is than with the details of the coefficients. If it's a low-pass filter and you want it to be scaled the same as the ADC input and it has a DC gain of 1 -- no, you don't have to shift the output. This could happen with coefficents that are Q6.10, Q2.14, Q1.15 or many other Qwhatever.whatever.
You need to find your filter's transfer function, and find out what it's supposed to be doing -- then you'll know.