I normally play straight up death/black metal so don't use alot of effects, but I play lead guitar now and am interested in playing more gothic sounding leads ala Gregor Mackintosh

https://youtu.be/vQcAvJaJz_w

And especially this band

https://youtu.be/UhwpsfvNq6s

I want to know how to get a guitar tone similar to these albums, the only effect pedal I really use is a flanger but I don't really know how to use it. I'm also using OD with high treble/mid.

Maybe go try a chorus pedal at a music store, if possible? I'm not really sure how applicable it would be to Septic Flesh, but that's definitely something I'd consider part of the gothic metal lead guitar tone.

For heavy use of the chorus effect in guitars, see Star Rover by The Loveless (it's sorta gothic rock):
https://www.youtube.com/watch?v=xgZVut5efsM
https://www.youtube.com/watch?v=e9Lqeew5nLc

That lead guitar on Gothic does sound like there's a flanger, but the effect is more subtle. A chorus effect can achieve a similar feeling, and in my opinion, sounds more appropriate for gothic stuff. Chorus gives the feeling of the note going slightly in and out of tune, whereas flanger doesn't necessarily do that.

You might want to look at some tutorials on those effects on Youtube if you're not sure how to use them to get the effect you want.

If you could link to a particular part in the Septic Flesh album that sounds like what you want, that would be helpful. That album has lots of stuff going on, and the lead guitars can be a little buried.

The parts in that Septicflesh album I'm talking about are 8:45 and 31:10.

I bought a flanger with more Fields of the Nephilim stuff in mind, but maybe I'll need chorus and delay to get more of this gothic metal sound.

Sounds like you need a bit of chorus, a lot of leads use the effect to some extent. Try cutting down the mids, too, see how that sounds.

Scoop out the mids and work on your vibrato, its all in the fingers!

I haven't gotten around to getting a chorus yet (the stores around here don't have any in stock) but I did turn down my mids and turned up the treble quite a bit and my guitar is just slicing through the mix like butter! Not to mention the flanger sounds a lot more clear