For editing gaps, you might need to make multiple sequence alignment and look at the sequence conservation. Some information can be found here.
For Secondary structure prediction Psipred and Jpred are highly recommended.
In addition, you can look into Expasy repository for a number of prediction tools Expasy tools
Have a look at this nature article. By the way, may I ask why you only want to learn through Swiss PDB or Deep View and why not modeller or I-Tasser. Although I-Tasser is an automated server but you can still provide your own alignment of target and template. You must be knowing, quality of alignment is crucial for good modelling, which indeed means selection of good templates.
It is worth trying different softwares for modelling and then compare it by evaluating on servers like SAVS or others.