normally quoque comes after the word it’s referred to.
So you could say: In oppido nostro ecclesia quoque inest.
In this case you mean that there is also a church in your town = even a church. In this case I would even use etiam instead of quoque: In oppido nostro etiam ecclesia est! But the meaning is a bit strange to me: in fact in this way you seem to want to emphasize that there is even a church in your town, something unusual that other towns don’t have or what do you mean exactly?
If you want to say that also your town has a church, like most of the other towns, the quoque should refer to in oppido nostro and then you have: Ecclesia in oppido nostro quosue (in)est.
I think the real difficulty comes in using EST at the beginning of the sentence. Though, this is certainly classical, although uncommon. The position of QVOQVE in your original sentence though really seems the most natural to me, merely since EST is first. But, like suggested above, if you wrote:
In oppido nostro ecclesia quoque est.
But this seems stilted to me. Instead:
In oppido nostro ecclesia est quoque.
I probably wouldn’t use QVOQVE at all though, and opt instead for etiam, item, or something more colorful.
“est” is placed just where it should be in your sentence Kemberg. When forms of “sum” are acting as a substantive verb, they regularly stand first in the sentence (see Allen & Greenough 598 c.). Since there is no predicate noun or adjective, est is placed properly.
In your phrase you can indeed put ‘est’ in front. When ‘est’ is in front of a phrase it is mostly indeed a substantive verb, like A&G says. But we can even specify this. ‘Est’ is mostly situated in front of a phrase when it is a substantive verb and specifically when it means ‘to exist’. But also in this sense it can sometimes have an other place. For Allen and Greenough, cf. http://www.perseus.tufts.edu/cgi-bin/ptext?doc=Perseus%3Atext%3A1999.04.0001;layout=;loc=;query=toc