There are number of issues that you need to address.
First, is this a performance ("concert") video or a music video; these are two
VERY different things. A performance video is a live performance captured on "tape." A music video is lip-syncing/playing to a prerecorded audio track.
The ultimate "perfect" concert video will have a multi-track recording of the individual instruments and vocals that will be re-mixed after the show. This, of course, is not usually an option for club bands, etc.
The next best thing is to record the audio from the FOH (Front of House) mixing console. The problem here is that in smaller (and even much larger) venues the FOH mix is mixed so the band sounds great in the room, it is
not for later reproduction. This means that in a small or even medium sized room the mix captured off of the FOH console will most probably be very unbalanced; the guitar player may be playing very loud so may be very quiet or almost non-existent in the FOH mix except for what is picked up by the other mics on stage, and that will be flukey as the singers move on and off of the vocal mics, and can get especially weird if the lead vocalist walks around the stage, holds his/her mic to the side or points it towards the audience when not singing, for example. In very small rooms it is not at all unusual for just the vocals and the kick drum to be miced, and that is all you will get from the FOH mix.
You can use one or two mics aimed at the PA cabinets and/or the stage for a better blend. However, if the mics are very close you may not get good representation from the lower end of the audio frequency spectrum (bass and kick drum, for example) as low sounds need more space to propagate. As you move further back, however, the issue becomes crowd noise. In this instance you need to find a balance between the two, a compromise that is never wholly satisfactory. (BTW, the mics of the DR-40 are woefully inadequate to the task.)
If you have more audio tracks available you can record the FOH mix direct
and the PA/Stage mix with mics, then blend the two together during post. It is also very nice to have a pair of audience mics. The best I ever accomplished in a medium sized room was a mix off of the FOH console, a pair of mics above and about ten feet in front of the stage, a pair of mics directly in front of the FOH console (the best mix, as this is what the FOH engineer is hearing but with a fair amount of crowd noise) and a pair of crowd mics for a total of eight (

audio tracks. It took a while to correct for phasing issues as they were not perfectly in sync; sound
does take time to go from the front to the back of the room. When I "mixed" the show I made multiple copies of the stage and FOH audio tracks and then used EQ to bring out and even reduce certain instruments a little bit. That took almost as long as mixing for individual instruments.
Once again, this is something that takes practice and experience to get right. See if the band has a couple of audio recorders (most bands record rehearsals) and a few extra mics. Maybe their live mix engineer, if they have a regular guy/gal, can do the post audio for you.