RNASeq analysis using featureCount and EdgeR

I am using a pipeline (bam -> featurecount-> EdgeR) to do some RNASeq analysis of several groups and sub-groups. For example, I have the following dataset with two types (T1 and T2) and T1 has three groups G1, G2 and G3, T2 has G5 and G6 groups. I would like to find TPM numbers, fold-change and FDR for all the genes and Groups.

Type Group SRA_Run#
T1   G1.   <some SRA ids e.g. SRR123456, SRR112233>
T1   G2.   <some SRA>
T1.  G3.   <some SRA>
T2.  G5.   <some SRA>
T2.  G6.   <some SRA>

I have individual BAM files generated for each SRA Run. I also individual read counts from featureCount for each SRA Run. I was not sure if I need to merge individual read counts for each group or run featureCount using all bam files of a group at once. Does it make any difference in the analysis that follows.

I also would like to know if I can run EdgeR at once for all the types and groups at once for doing differential gene expression for each group of Type 1 (T1) against every other group of Type 2 (T2). I am bit stuck at this point how to proceed. Any help would be appreciated.