My plasmid contains a SV40 origin and a Neo selection marker; if I select 293T cells I have to use another antibiotic (and make a co-transfection with a second plasmid for the selection), if I use 293 cells, will my selected lines be stable for a long time range (as the T antigen transduction in 293T is mainly helping in expression and maintenance of SV40 origin containing plasmids)?
In my experience, the stability of expression over time is dependent upon a lot of different things, for example:
>where in the genome your plasmid incorporates
>what cell line you use (some are more effective at silencing than others)
>the promoter that you use
>gene toxicity (is it a survival advantage to not express the gene)
I have cell lines that I do not need to select at all and they maintain high expression over many months, so in that case, it clearly would not have an effect whether the selection marker is on the same or a separate plasmid. I have also had clones that are expressing the target gene and selection marker on the same plasmid that lose target gene expression while retaining selection marker resistance (either selective promoter silencing or selection of target gene mutants with a survival advantage). Finally, I have transfected 293T cells with two plasmids as you suggest (with SV40ori on the target gene plasmid), and selected clones that show stable target gene expression.
In my experience the biggest disadvantage of this two-plasmid approach is that you need to screen more clones to find those that express. There may also be a somewhat higher risk of these clones being unstable, but it is certainly not absolute. I would in any case give it a try if you don't have the possibility of transferring your target gene to a plasmid with a different resistance marker.
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