The primary goal of Unipro UGENE project is the integration of most popular computational biology analysis methods within single user-friendly visual interface. UGENE is a
free software. Full feature list can be found at the
UGENE web-page. There is also
a presentation available on the web, feel free to check it out.
Concerning Gmap: you are quite right, it is applied for EST (cDNA) and mRNA sequence alignment, while Bowtie is a "general DNA" short read aligner. Also Gmap performs genome mapping. However, I suppose Bowtie can be used for your alignment task. It is a memory-efficient and very fast short-read aligner. You can read more about Bowtie
here.
To use Bowtie from UGENE, activate Tools->DNA assembly dialog from main menu. Select Bowtie as assembly method, then set path to your reference genome and your cDNA shortreads. Additionaly you can use a prebuilt-index for genome (there is an optional check box). The pre-built indecies are available from official Bowtie
ftp.
Don't forget to read UGENE
manual pages devoted to Bowtie.
Btw UGENE user manual is available as a printable
PDF file. It's the best source of information about UGENE.